Read by QxMD icon Read

computational chemistry

Richard A Manderville, Stacey D Wetmore
The formation of DNA adducts by the attack of intermediates derived from toxic substances at the C8 position of 2-deoxyguanosine (dG) is a common damaging event. Although the majority of studies on C8-dG adducts have focused on lesions containing a C8-N-C tether between the bulky moiety and the nucleobase, the formation of O-linked lesions with a similar tether topology and C-linked adducts involving direct C8-C connectivity have also been uncovered. Several studies have been done to try to better understand the structural impact and mutagenicity of O-linked and C-linked aryl C8-dG adducts, including lesions arising from unsubstituted and chloro substituted phenols, and the food mutagen ochratoxin A (OTA)...
October 21, 2016: Chemical Research in Toxicology
Yin-Shan Meng, Shang-Da Jiang, Bing-Wu Wang, Song Gao
Single-molecule magnets (SMMs) can retain their magnetization status preferentially after removal of the magnetic field below a certain temperature. The unique property, magnetic bistable status, enables the molecule-scale SMM to become the next-generation high-density information storage medium. SMMs' new applications are also involved in high-speed quantum computation and molecular spintronics. The development of coordination chemistry, especially in transition metal (3d) and lanthanide (4f) complexes, diversifies SMMs by introducing new ones...
October 21, 2016: Accounts of Chemical Research
Arnab Rit, Jesús Campos, Haoyu Niu, Simon Aldridge
Vinylidene (H2C=C) is a member of the family of compounds of composition CH (and isomeric with ethyne, HC≡CH), but it has been observed only transiently-with a lifetime in the region of 0.1 ns. Indeed, no simple (non-base-stabilized) compounds of the type R2E=E have been characterized structurally for any of the group 14 elements. Here we show that by employing the bulky and strongly electron-donating boryl ligand (HCDippN)2B (Dipp, 2,6-(i)Pr2C6H3), a simple monomeric digermavinylidene compound, (boryl)2GeGe, can be synthesized and is stable at room temperature...
November 2016: Nature Chemistry
Giorgio Lanzani, Ari P Seitsonen, Marcella Iannuzzi, Kari Laasonen, Simo Olavi Pehkonen
The chemistry of aluminium or oxo-aluminium in water is still relatively unknown, although it is the basis for many chemical and industrial processes, including floc- culation in water treatment plants. Trimeric species have a predominant role in the formation of the Keggin cations, which are the basic building block of aluminium- based chemicals. Despite this, the details of the structural evolution of these small solvated clusters and how this is related to the processes leading to the formation of larger aggregates is still an open issue...
October 21, 2016: Journal of Physical Chemistry. B
Tiecheng Zhou, Joshua J Goings, Zhou Lin
No abstract text is available yet for this article.
October 21, 2016: Journal of Physical Chemistry. A
Federica Lanni, Andrea Carotti, Roccaldo Sardella, Antonio Macchiarulo, Lucia Pucciarini, Benedetto Natalini
In the last few decades, there has been a significant increase in the development of chiral compounds. Thus, access to enantiomerically pure compounds is currently a major focus of pharmaceutical research and, in particular, chiral HPLC separations have gained great importance for semi-preparative and industrial isolation of enantiopure compounds. Chemoinformatic procedures as well as molecular modelling and quantum chemistry techniques can be successfully applied to address chirality related problems especially when enantiomerically pure reference standards are missing...
October 18, 2016: Mini Reviews in Medicinal Chemistry
Noor Asidah Mohamed, Richard T Bradshaw, Jonathan W Essex
The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field...
October 19, 2016: Journal of Computational Chemistry
Craig Waitt, Nashali M Ferrara, Henk Eshuis
The performance of the random phase approximation (RPA) is tested for ther- mochemistry and geometries of transition metal chemistry using various benchmarks obtained either computationally or experimentally. Comparison is made to popular (semi-)local, meta- and hybrid density functionals as well as to second-order Møller- Plesset perturbation theory (MP2) and its spin-component-scaled derivatives. The benchmarks sets include reaction energies, barrier heights and dissociation energies of prototype bond-activation reactions, dissociation energies for a set of large transition metal complexes, bond lengths and dissociation energies of metal hydride ions, and bond lengths and angles of a set of closed-shell first-row transition metal complexes...
October 17, 2016: Journal of Chemical Theory and Computation
James McDonagh, David S Palmer, Tanja Van Mourik, John B O Mitchell
We compare a range of computational methods for the prediction of sublimation thermodynamics (enthalpy, entropy and free energy of sublimation). These include a model from theoretical chemistry that utilizes crystal lattice energy minimization (with the DMACRYS program) and QSPR models generated by both machine learning (Random Forest and Support Vector Machines) and regression (Partial Least Squares) methods. Using these methods we investigate the predictability of the enthalpy, entropy and free energy of sublimation, with consideration of whether such a method may be able to improve solubility prediction schemes...
October 17, 2016: Journal of Chemical Information and Modeling
John Lee
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria, and those utilizing imidazopyrazinone luciferins such as coelenterazine, are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography, and computational chemistry. The chemical structures of all reactants are well defined and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter...
October 17, 2016: Photochemistry and Photobiology
Mengzhe Guo, Dengyang Yin, Jie Han, Cheng Guo, Xiao Li, Liyan Zhang, Yan Du, Haibo Wang, Daoquan Tang
RATIONALE: Mass spectrometry has been developed as one of the common tools for the analysis of the organometallic systems in the gas phase over decades. The study of the fragmentation of organics-metal complexes has attracted much attention since the interesting dissociation pathways exhibited by these compounds are usually different from the protonated analogues. METHODS: In this work, iohexol complexed with different dications such as Mg(2+) , Cu(2+) , and Zn(2+) have been investigated by ESI tandem mass spectrometry...
October 17, 2016: Rapid Communications in Mass Spectrometry: RCM
Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
The C-terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non-neutralized. Because of the flexibility of the unbound CTD, a free-energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized...
December 5, 2016: Journal of Computational Chemistry
Sapna Cheryan, Sianna A Ziegler, Amanda K Montoya, Lily Jiang
Women obtain more than half of U.S. undergraduate degrees in biology, chemistry, and mathematics, yet they earn less than 20% of computer science, engineering, and physics undergraduate degrees (National Science Foundation, 2014a). Gender differences in interest in computer science, engineering, and physics appear even before college. Why are women represented in some science, technology, engineering, and mathematics (STEM) fields more than others? We conduct a critical review of the most commonly cited factors explaining gender disparities in STEM participation and investigate whether these factors explain differential gender participation across STEM fields...
October 10, 2016: Psychological Bulletin
Sandra Osburn, Bun Chan, Victor Ryzhov, Leo Radom, Richard A J O'Hair
Experimental and computational quantum chemistry investigations of the gas-phase ion-molecule reactions between the distonic ions (+)H3N(CH2)nS(•) (n = 2-4) and the reagents dimethyl disulfide, allyl bromide, and allyl iodide demonstrate that intramolecular hydrogen bonding can modulate the reactivity of thiyl radicals. Thus, the 3-ammonium-1-propanethiyl radical (n = 3) exhibits the lowest reactivity of these distonic ions toward all substrates. Theoretical calculations on this distonic ion highlight that its most stable conformation involves a six-membered ring configuration, and that it has the strongest intramolecular hydrogen bond...
October 11, 2016: Journal of Physical Chemistry. A
Peng Dai, Chi Zhang, Matthew Welborn, James J Shepherd, Tianyu Zhu, Troy Van Voorhis, Bradley L Pentelute
Highly efficient and selective chemical reactions are desired. For small molecule chemistry, the reaction rate can be varied by changing the concentration, temperature, and solvent used. In contrast for large biomolecules, the reaction rate is difficult to modify by adjusting these variables because stringent biocompatible reaction conditions are required. Here we show that adding salts can change the rate constant over 4 orders of magnitude for an arylation bioconjugation reaction between a cysteine residue within a four-residue sequence (π-clamp) and a perfluoroaryl electrophile...
September 28, 2016: ACS Central Science
Lili Du, Xiting Zhang, Jiadan Xue, Wen-Jian Tang, Mingde Li, Xin Lan, Jiangrui Zhu, Ruixue Zhu, Yuxiang Weng, Yunliang Li, David Lee Phillips
Quinone methides (QM) are crucial reactive species in molecular biology and organic chemistry, with little known regarding the mechanism(s) for the generation of short-lived reactive QM intermediates from relevant precursors in aqueous solutions. In this study, several time-resolved spectroscopy methods were used to directly examine the photophysics and photochemical pathways of 1,1'-(2,2'-dihydroxy-1,1'-binaphthyl-6,6'-diyl)bis(N,N,N-trimethylmethanaminium) bromide (BQMP-b) from initial photoexcitation to the generation of the key reactive binol QM intermediate (BQM) in aqueous solution...
October 10, 2016: Journal of Physical Chemistry. B
Amol Baliram Patil, Bhalchandra Mahadeo Bhanage
Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Oleg Kostko, Tyler P Troy, Biswajit Bandyopadhyay, Musahid Ahmed
Proton transfer in aqueous media is a ubiquitous process, occurring in acid-base chemistry, biology, and in atmospheric photochemistry. Photoionization mass spectrometry coupled with theoretical calculations demonstrate that a relay-type proton transfer mechanism is operational for single-water-molecule-assisted proton transfer between two acetaldehyde molecules in the gas phase. Threshold photoionization of acetaldehyde-water clusters leads to proton transfer between the formyl groups (-CH[double bond, length as m-dash]O) of one acetaldehyde molecule to another, and the subsequent formation of cationic moieties...
September 14, 2016: Physical Chemistry Chemical Physics: PCCP
Andrew J Logsdail, Christopher A Downing, Thomas W Keal, Paul Sherwood, Alexey A Sokol, C Richard A Catlow
We have investigated the energetic properties of Mn-doped MgO bulk and (100) surfaces using a QM/MM embedding computational method, calculating the formation energy for doped systems, as well as for surface defects, and the subsequent effect on chemical reactivity. Low-concentration Mn doping is endothermic for isovalent species in the bulk but exothermic for higher oxidation states under p-type conditions, and compensated by electrons going to the Fermi level rather than cation vacancies. The highest occupied dopant Mn 3d states are positioned in the MgO band gap, about 4...
October 6, 2016: Physical Chemistry Chemical Physics: PCCP
Michiko Tawada, Shinkichi Suzuki, Yasuhiro Imaeda, Hideyuki Oki, Gyorgy Snell, Craig A Behnke, Mitsuyo Kondo, Naoki Tarui, Toshimasa Tanaka, Takanobu Kuroita, Masaki Tomimoto
A novel approach was conducted for fragment-based lead discovery and applied to renin inhibitors. The biochemical screening of a fragment library against renin provided the hit fragment which showed a characteristic interaction pattern with the target protein. The hit fragment bound only to the S1, S3, and S3(SP) (S3 subpocket) sites without any interactions with the catalytic aspartate residues (Asp32 and Asp215 (pepsin numbering)). Prior to making chemical modifications to the hit fragment, we first identified its essential binding sites by utilizing the hit fragment's substructures...
September 28, 2016: Bioorganic & Medicinal Chemistry
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"