920 results match your criteria stable computations

Dioxygen Activation and Pyrrole α-Cleavage with Calix[4]pyrrolato Aluminates: Enzyme Model by Structural Constraint.

Angew Chem Int Ed Engl 2021 May 6. Epub 2021 May 6.

Ruprecht Karls Universitat Heidelberg Fakultät für Chemie und Geowissenschaften, Inorganic Chemistry Departement, Institut für Anorganische Chemie, Im Neuenheimer Feld 270, 69120, Heidelberg, GERMANY.

The present work describes the reaction of triplet dioxygen with the porphyrinogenic calix[4]pyrrolato aluminates to alkylperoxido aluminates in high selectivity. Multiconfigurational quantum chemical computations disclose the mechanism for this spin-forbidden process. Despite a negligible spin-orbit coupling constant, the intersystem crossing (ISC) is facilitated by singlet and triplet state degeneracy and spin-vibronic coupling. Read More

View Article and Full-Text PDF

1,1,2-Ethenetriol: The Enol of Glycolic Acid, a High-Energy Prebiotic Molecule.

Angew Chem Int Ed Engl 2021 May 5. Epub 2021 May 5.

Justus-Liebig University, Institute of Organic Chemistry, Heinrich-Buff-Ring 58, 35392, Giessen, GERMANY.

As low temperature conditions (e.g., in space) prohibit reactions requiring large activation energies, an alternative mechanism for follow-up transformations of highly stable molecules involves the reactions of higher-energy isomers that were generated in a different environment. Read More

View Article and Full-Text PDF

Computational Study of Hydrogen Bond Interactions in Water Cluster-Organic Molecule Complexes.

J Phys Chem A 2021 Apr 20;125(16):3369-3377. Epub 2021 Apr 20.

Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7.

We analyzed the interactions present in complexes that acetone, azomethane, dimethylamine, dimethyl ether, methyl acetate, and oxirane form with 39 different (HO) clusters ( = 1-10). A random generation of configurations and a subsequent screening procedure were employed to sample representative interactions. Using quantum chemical computations, we calculated the associated binding energies, which range from -0. Read More

View Article and Full-Text PDF

Robust Gold Nanocluster Protected with Amidinates for Electrocatalytic CO2 Reduction.

Angew Chem Int Ed Engl 2021 Apr 19. Epub 2021 Apr 19.

Tsinghua University, Chemistry Department, 1 Tsinghua Yuan, Haidian District, 100084, Beijing, CHINA.

The first all-amidinate-protected gold nanocluster [Au28(Ph-form)12](OTf)2 (Ph-form = N,N'-Diphenylformamidine) ( Au28 ) has been synthesized and structurally resolved. Single crystal X-ray diffraction reveals that Au28 has a compact Au4@Au24 tetrahedral core-shell structure of T symmetry, which is fully protected by 12 bridging formamidinate ligands. This cluster is quite robust as indicated by the fact that it can stay intact in solution at 80 °C for 6 d. Read More

View Article and Full-Text PDF

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases.

Molecules 2021 Mar 20;26(6). Epub 2021 Mar 20.

CNR-Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.

We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. Read More

View Article and Full-Text PDF

MX Anti-MXenes from Non-van der Waals Bulks for Electrochemical Applications: The Merit of Metallicity and Active Basal Plane.

ACS Nano 2021 Apr 18;15(4):6233-6242. Epub 2021 Mar 18.

Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico 00931, United States.

Two-dimensional transition-metal compounds (2DTMCs) are promising materials for electrochemical applications, but 2DTMCs with metallicity and active basal planes are rare. In this work, we proposed a simple and effective strategy to extract 2DTMCs from non-van der Waals bulk materials and established a material library of 79 2DTMCs, which we named as anti-MXenes since they are composed of one M atomic layer sandwiched by two X atomic layers. By means of density functional theory computations, 24 anti-MXenes were confirmed to be thermodynamically, dynamically, mechanically, and thermally stable. Read More

View Article and Full-Text PDF

Identification of earth-abundant materials for selective dehydrogenation of light alkanes to olefins.

Proc Natl Acad Sci U S A 2021 Mar;118(11)

SUNCAT Center for Interface Science and Catalysis, Stanford Linear Accelerator Center, Menlo Park, CA 94025;

Selective ethane dehydrogenation (EDH) is an attractive on-purpose strategy for industrial ethylene production. Design of an effective, stable, and earth-abundant catalyst to replace noble metal Pt is the main obstacle for its large-scale application. Herein, we report an experimentally validated theoretical framework to discover promising catalysts for EDH, which combines descriptor-based microkinetic modeling, high-throughput computations, machine-learning concepts, and experiments. Read More

View Article and Full-Text PDF

Synthesis and Thermal Study of Hexacoordinated Aluminum(III) Triazenides for Use in Atomic Layer Deposition.

Inorg Chem 2021 Apr 12;60(7):4578-4587. Epub 2021 Mar 12.

Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden.

Amidinate and guanidinate ligands have been used extensively to produce volatile and thermally stable precursors for atomic layer deposition. The triazenide ligand is relatively unexplored as an alternative ligand system. Herein, we present six new Al(III) complexes bearing three sets of a 1,3-dialkyltriazenide ligand. Read More

View Article and Full-Text PDF

SO ( = 0, 1, and 2) Molecular Systems: Characterization and Atmospheric Planetary Implications.

J Phys Chem A 2021 Mar 26;125(9):1958-1971. Epub 2021 Feb 26.

Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes 77454, Champs sur Marne, France.

We use accurate methodologies at the coupled cluster level ((R)CCSD(T)) and its explicitly correlated version ((R)CCSD(T)-F12) to investigate the electronic structure, relative stability, and spectroscopy of the stable isomers of the [SO] system and of some of its cations and dications, with a special focus on the most relevant isomers that could be involved in terrestrial and planetary atmospheres. This work identifies several stable isomers (10 neutral, 8 cationic, and 5 dicationic), including -OSSO, -OSSO, and -OSSO. For all these isomers, we calculated geometric parameters, fragmentation energies, and simple and double ionization energies of the neutral species. Read More

View Article and Full-Text PDF

Intrinsic Disruption of the M1 Cortical Network in a Mouse Model of Parkinson's Disease.

Mov Disord 2021 Feb 19. Epub 2021 Feb 19.

The Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.

Background: Parkinson's disease (PD) disrupts motor performance by affecting the basal ganglia system. Yet, despite the critical position of the primary motor cortex in linking basal ganglia computations with motor performance, its contribution to motor disability in PD is largely unknown. The objective of this study was to characterize the role of the primary motor cortex in PD-related motor disability. Read More

View Article and Full-Text PDF
February 2021

Three-dimensional nonlinear dynamics of prestressed active filaments: Flapping, swirling, and flipping.

Phys Rev E 2021 Jan;103(1-1):013005

Department of Mechanical Engineering, University of California, Merced, California 95343, USA and Health Sciences Research Institute, University of California, Merced, California 95343, USA.

Initially straight slender elastic filaments or rods with constrained ends buckle and form stable two-dimensional shapes when prestressed by bringing the ends together. Beyond a critical value of this prestress, rods can also deform off plane and form twisted three-dimensional equilibrium shapes. Here, we analyze the three-dimensional instabilities and dynamics of such deformed filaments subject to nonconservative active follower forces and fluid drag. Read More

View Article and Full-Text PDF
January 2021

A Network Thermodynamic Analysis of Amyloid Aggregation along Competing Pathways.

Appl Math Comput 2021 Mar 18;393. Epub 2020 Nov 18.

Department of Mathematics, Montclair State University, Montclair, NJ 07043.

Aggregation of proteins towards amyloid formation is a significant event in many neurodegenerative diseases. Low-molecular weight oligomers are considered to be the primary toxic agents in many of these maladies. Therefore, there is an increasing interest in understanding their formation and behavior. Read More

View Article and Full-Text PDF

Binding of azobenzene and p-diaminoazobenzene to the human voltage-gated sodium channel Na1.4.

Phys Chem Chem Phys 2021 Feb 29;23(5):3552-3564. Epub 2021 Jan 29.

Department of Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain.

The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Na1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Read More

View Article and Full-Text PDF
February 2021

Computational density-functional approaches on finite-size and guest-lattice effects in CO@sII clathrate hydrate.

J Chem Phys 2021 Jan;154(4):044301

Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.

We performed first-principles computations to investigate guest-host/host-host effects on the encapsulation of the CO molecule in sII clathrate hydrates from finite-size clusters up to periodic 3D crystal lattice systems. Structural and energetic properties were first computed for the individual and first-neighbors clathrate-like sII cages, where highly accurate ab initio quantum chemical methods are available nowadays, allowing in this way the assessment of the density functional (DFT) theoretical approaches employed. The performance of exchange-correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. Read More

View Article and Full-Text PDF
January 2021

Nonpolarizing oxygen-redox capacity without O-O dimerization in NaMnO.

Nat Commun 2021 Jan 27;12(1):631. Epub 2021 Jan 27.

Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656, Japan.

Reversibility of an electrode reaction is important for energy-efficient rechargeable batteries with a long battery life. Additional oxygen-redox reactions have become an intensive area of research to achieve a larger specific capacity of the positive electrode materials. However, most oxygen-redox electrodes exhibit a large voltage hysteresis >0. Read More

View Article and Full-Text PDF
January 2021

Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Apr 29;251:119388. Epub 2020 Dec 29.

Department of Physics and Research Centre, Scott Christian College (Autonomous), Nagercoil 629003, Tamil Nadu, Affiliated to Manonmaniam Sundarnar University, Abishekapatti, Tirunelveli 627012, India. Electronic address:

Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Read More

View Article and Full-Text PDF

What does graphitic carbon nitride really look like?

Phys Chem Chem Phys 2021 Feb;23(4):2853-2859

Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, CNRS, 46 allée d'Italie, F-69007 Lyon Cedex, France.

Graphitic carbon nitrides (g-CNs) have become popular light absorbers in photocatalytic water splitting cells. Early theoretical work on these structures focused on fully polymerized g-C3N4. Experimentally, it is known that the typically employed melamine polycondensation does not go toward completion, yielding structures with ∼15 at% hydrogen. Read More

View Article and Full-Text PDF
February 2021

Cheminformatics-Based Identification of Potential Novel Anti-SARS-CoV-2 Natural Compounds of African Origin.

Molecules 2021 Jan 14;26(2). Epub 2021 Jan 14.

Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA.

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome virus 2 (SARS-CoV-2) has impacted negatively on public health and socioeconomic status, globally. Although, there are currently no specific drugs approved, several existing drugs are being repurposed, but their successful outcomes are not guaranteed. Therefore, the search for novel therapeutics remains a priority. Read More

View Article and Full-Text PDF
January 2021

PID++: A Computationally Lightweight Humanoid Motion Control Algorithm.

Sensors (Basel) 2021 Jan 11;21(2). Epub 2021 Jan 11.

Department of Computer Science & Engineering, University of Bridgeport, Bridgeport, CT 06604, USA.

Currently robotic motion control algorithms are tedious at best to implement, are lacking in automatic situational adaptability, and tend to be static in nature. Humanoid (human-like) control is little more than a dream, for all, but the fastest computers. The main idea of the work presented in this paper is to define a radically new, simple, and computationally lightweight approach to humanoid motion control. Read More

View Article and Full-Text PDF
January 2021

Infrared Multiple Photon Dissociation Spectroscopy of Protonated Cyameluric Acid.

J Phys Chem A 2021 Jan 7;125(2):607-614. Epub 2021 Jan 7.

INFIQC (CONICET - Universidad Nacional de Córdoba), Ciudad Universitaria, X5000HUA Córdoba, Argentina.

The present study reports the first structural characterization of protonated cyameluric acid ([CA + H]) in the gas phase, which paves the way for prospective bottom-up research on the condensed-phase chemistry of CA in the protonated form. A number of [CA + H] keto-enol isomers can a priori be produced as a result of protonation at available N and O positions of precursor neutral CA tautomers, yet ab initio computations predict different reduced [CA + H] isomer populations dominating the solution and gas phases that are involved in the ion generation process (i.e. Read More

View Article and Full-Text PDF
January 2021

Pressure effects on electronic, elastic, and vibration properties of metallic antiperovskite PbNCa by ab initio calculations.

J Mol Model 2021 Jan 3;27(1). Epub 2021 Jan 3.

Physics Department, Faculty of Arts and Sciences, Amasya University, 05100, Amasya, Turkey.

Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of states, elastic properties, and phonon frequencies for PbNCa have been examined. We have obtained some concerned feature as Young modulus and Poisson ratio for this compound using the elastic parameters. Read More

View Article and Full-Text PDF
January 2021

Optimal dimensionality reduction of Markov chains using graph transformation.

J Chem Phys 2020 Dec;153(24):244108

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

Markov chains can accurately model the state-to-state dynamics of a wide range of complex systems, but the underlying transition matrix is ill-conditioned when the dynamics feature a separation of timescales. Graph transformation (GT) provides a numerically stable method to compute exact mean first passage times (MFPTs) between states, which are the usual dynamical observables in continuous-time Markov chains (CTMCs). Here, we generalize the GT algorithm to discrete-time Markov chains (DTMCs), which are commonly estimated from simulation data, for example, in the Markov state model approach. Read More

View Article and Full-Text PDF
December 2020

Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions.

Molecules 2020 Dec 23;26(1). Epub 2020 Dec 23.

Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia.

Despite the technological importance of urea perhydrate (percarbamide) and sodium percarbonate, and the growing technological attention to solid forms of peroxide, fewer than 45 peroxosolvates were known by 2000. However, recent advances in X-ray diffractometers more than tripled the number of structurally characterized peroxosolvates over the last 20 years, and even more so, allowed energetic interpretation and gleaning deeper insight into peroxosolvate stability. To date, 134 crystalline peroxosolvates have been structurally resolved providing sufficient insight to justify a first review article on the subject. Read More

View Article and Full-Text PDF
December 2020

Two-dimensional GaO monolayer with tunable band gap and high hole mobility.

Phys Chem Chem Phys 2021 Jan;23(1):666-673

School of Materials, Zhengzhou University of Aeronautics, Zhengzhou 450015, China.

By means of density functional theory and unbiased structure search computations, we systematically investigated the stability and electronic properties of a new Ga2O2 monolayer. The phonon spectra and ab initio molecular dynamics simulations show that the Ga2O2 monolayer is dynamically and thermally stable. Moreover, it also shows superior open-air stability. Read More

View Article and Full-Text PDF
January 2021

High-Efficiency Thermal-Annealing-Free Organic Solar Cells Based on an Asymmetric Acceptor with Improved Thermal and Air Stability.

ACS Appl Mater Interfaces 2020 Dec 8;12(51):57271-57280. Epub 2020 Dec 8.

Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China.

The stability of organic solar cells (OSCs) is an urgent problem for commercialization. In this work, a novel asymmetric molecule TB-4Cl was designed and synthesized. Quantum chemical computations revealed that TB-4Cl has a larger dipole moment of 1. Read More

View Article and Full-Text PDF
December 2020

Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra.

Environ Sci Technol 2020 12 3;54(24):15904-15913. Epub 2020 Dec 3.

Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Read More

View Article and Full-Text PDF
December 2020

Head phantoms for bioelectromagnetic applications: a material study.

Biomed Eng Online 2020 Nov 23;19(1):87. Epub 2020 Nov 23.

Institute of Biomedical Engineering and Informatics, Faculty of Computer Science and Automation, Technische Universität Ilmenau, 98693, Ilmenau, Germany.

Background: Assessments of source reconstruction procedures in electroencephalography and computations of transcranial electrical stimulation profiles require verification and validation with the help of ground truth configurations as implemented by physical head phantoms. For these phantoms, synthetic materials are needed, which are mechanically and electrochemically stable and possess conductivity values similar to the modeled human head tissues. Three-compartment head models comprise a scalp layer with a conductivity range of 0. Read More

View Article and Full-Text PDF
November 2020

Ring-closing metathesis of prochiral oxaenediynes to racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2-pyrans.

Beilstein J Org Chem 2020 13;16:2757-2768. Epub 2020 Nov 13.

Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic.

The prochiral 4-(allyloxy)hepta-1,6-diynes, optionally modified in the positions 1 and 7 with an alkyl or ester group, undergo a chemoselective ring-closing enyne metathesis yielding racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2-pyrans. Among the catalysts tested, Grubbs 1st generation precatalyst in the presence of ethene (Mori conditions) gave superior results compared to the more stable Grubbs or Hoveyda-Grubbs 2nd generation precatalysts. This is probably caused by a suppression of the subsequent side-reactions of the enyne metathesis product with ethene. Read More

View Article and Full-Text PDF
November 2020

Modelling interactions of cationic dimers in He droplets: microsolvation trends in HeK clusters.

Phys Chem Chem Phys 2021 Apr 21;23(13):7849-7859. Epub 2020 Nov 21.

Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.

We report the results of a detailed theoretical investigation of small K-doped He clusters. The structural characteristics and stabilities of such cations are determined from ab initio electronic structure calculations at the MRCI+Q level of theory. The underlying interactions show a multireference character and such effects are analyzed. Read More

View Article and Full-Text PDF

Blue Phosphorene Bilayer Is a Two-Dimensional Metal and an Unambiguous Classification Scheme for Buckled Hexagonal Bilayers.

Phys Rev Lett 2020 Nov;125(19):196401

Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, 97310, Mérida, Yucatán, México.

High-level first-principles computations predict blue phosphorene bilayer to be a two-dimensional metal. This structure has not been considered before and was identified by employing a block-diagram scheme that yields the complete set of five high-symmetry stacking configurations of buckled honeycomb layers, and allows their unambiguous classification. We show that all of these stacking configurations are stable or at least metastable both for blue phosphorene and gray arsenene bilayers. Read More

View Article and Full-Text PDF
November 2020