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1دورية أكاديمية
مصطلحات موضوعية: Biophysics, Biochemistry, Neuroscience, Biotechnology, Evolutionary Biology, Ecology, Inorganic Chemistry, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, larger diffusion coefficients, form multiple σ, empirical dispersion corrections, dgdzvp basis sets, alkyl group hydrogens, multiple interactions within, molecular interactions among, acceptor type interactions, weak electrostatic interaction, 2 , emi ][ fsi, bulk liquid state, 1 ‑ ethyl, ion pair conformers, ion pair, fsi ]], stronger interactions, plane interactions, ion pairs, weaker attraction
الوصف: An understanding of the nature of molecular interactions among the ion pairs of 1-ethyl-3-methylimidazolium bis(fluorosulfonyl)imide [EMI[FSI]] can offer a starting point and significant insight into the more dynamic and multiple interactions within the bulk liquid state. In this context, close inspection of ion pair conformers can offer insight into the effects in bulk [EMI][FSI] liquid. The current work, therefore, gives a detailed analysis of the [EMI][FSI] ion pair conformers through analysis of the interaction energies, stabilization energies, and natural orbital of the ion pair conformers. The structures of the cations, anions, and cation–anion ion pairs of the conformers are optimized systematically by the ωB97X-D method with the DGDZVP basis sets, considering both the empirical dispersion corrections and the presence of a polar solvent, and the most stable geometries are obtained. The [FSI] − anions, unlike [TFSI] − anions, exist at the top position with respect to imidazolium rings. The presence of out-of-plane interactions between the [EMI] + and [FSI] − ions is in good agreement with the stronger interactions of the [FSI] − anions with alkyl group hydrogens. The presence of out-of-plane conformers could also be related to the interaction of the anion with the π clouds of the [EMI] + ring. In the [EMI] + cation, the aromatic ring is π-acidic due to the presence of a positive charge in the N 1 –C 1 –N 2 ring, which leads to the presence of [FSI] − anion donor [EMI] + π-acceptor type interactions. The [EMI] + cation and [FSI] − anions tend to form multiple σ* and π* interactions but reduce the strength of the individual contributions from a potential (linear) maximum. For the ion pair [EMI][FSI], the absolute value of the interaction energies is lower than the normal hydrogen bond energy (50 kJ/mol), which indicates that there is a very weak electrostatic interaction between the [EMI] + cations and [FSI] − anions. The weaker attraction between the [EMI] + and [FSI] − ions is suggested to contribute to ...
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2دورية أكاديمية
المصدر: Техника и технология пищевых производств, Vol 52, Iss 4, Pp 718-728 (2022)
مصطلحات موضوعية: acetylcholine, density functional theory, dispersion corrections, crystal and electronic structure, vibrational modes, Food processing and manufacture, TP368-456
الوصف: The ever-growing capabilities of computing systems and algorithms make the first-principle methods extremely important in such research fields as biologically active compounds and complex biological systems. They also facilitate the target search and prediction of new forms. The purpose of the study was to define the structural parameters and basic electronic and vibration characteristics of crystal acetylcholine halides (ACh-Hal). The study featured acetylcholine chloride and bromide (ACh-Hal). The theoretical analysis was based on the density functional theory (DFT) with gradient Perdew-Burke-Ernzerhof exchange-correlation functional (PBE) and a semi-empirical scheme for dispersion-accounting density functional (DFT+D3). The calculations made it possible to define the optimized parameters of the crystal lattice: a = 9.765 Å, b = 15.217 Å, c = 6.274 Å for orthorhombic acetylcholine chloride (ACh-Cl); a = 10.883 Å, b = 13.304 Å, c = 7.077 Å, 109.21° for monoclinic bromide (ACh-Br). The calculations also revealed atomic coordinates, bond lengths, valence, and torsion angles. As for the electronic structure, ACh-Hal proved to be dielectrics with a band gap of 4.734 and 4.405 eV. The effective charges of carbon atoms were highly anisotropic. The calculated vibration spectra confirmed the experimental data in the entire interval, while the dependence on the mass of the anion was especially prominent in the region of lattice vibrations. The first-principle DFT+D3 scheme made it possible to obtain reliable data on the basic properties of complex organic and biologically active systems.
وصف الملف: electronic resource
العلاقة: https://fptt.ru/en/issues/21089/21051Test/; https://doaj.org/toc/2074-9414Test; https://doaj.org/toc/2313-1748Test
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3دورية أكاديمية
المؤلفون: Dominique A. Wappett, Lars Goerigk
مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Physiology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, without dispersion corrections, separated hybrids ωb97m, double hybrids sos0, dispersion corrections improve, density functional approximations, d3 ( bj, closed shell systems, calculate reference values, averaged mean absolute, >)- based approaches, whole set based, robust across many, new benchmark set, results across, mme55 set, benchmark set, system sizes, strong performer, reliable compromise, metalloenzyme reactions, jacob ’, enzyme energetics
الوصف: We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO–CCSD( T )-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob’s ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
الإتاحة: https://doi.org/10.1021/acs.jctc.3c00558.s001Test
https://figshare.com/articles/journal_contribution/Benchmarking_Density_Functional_Theory_Methods_for_Metalloenzyme_Reactions_The_Introduction_of_the_MME55_Set/24535093Test -
4دورية أكاديمية
مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, without dispersion corrections, without dispersion correction, random phase approximation, gas phase energy, ethane dehydrogenation network, density functional theory, surface energies accurately, eight different functionals, ethane dehydrogenation reaction, activation energies, work questions, transition states, simultaneously predict, length increases, hybrid classes, dft functionals, cost ratio, catalytic application, also gives
الوصف: The Random Phase Approximation (RPA) is conceptually the most accurate Density Functional Approximation method, able to simultaneously predict both adsorbate and surface energies accurately; however, this work questions its superiority over DFT for catalytic application on hydrocarbon systems. This work uses microkinetic modeling to benchmark the accuracy of DFT functionals against that of RPA for the ethane dehydrogenation reaction on Pt(111). Eight different functionals, with and without dispersion corrections, across the GGA, meta-GGA and hybrid classes are evaluated: PBE, PBE-D3, RPBE, RPBE-D3, BEEF-vdW, SCAN, SCAN-rVV10, and HSE06. We show that PBE and RPBE, without dispersion correction, closely model RPA energies for adsorption, transition states, reaction, and activation energies. Next, RPA fails to describe the gas phase energy as unsaturation and chain-length increases in the hydrocarbon. Finally, we show that RPBE has the best accuracy-to-cost ratio, and RPA is likely not superior to RPBE or BEEF-vdW, which also gives a measure of uncertainty.
الإتاحة: https://doi.org/10.1021/acs.jpclett.3c02723.s002Test
https://figshare.com/articles/journal_contribution/Benchmarking_the_Accuracy_of_Density_Functional_Theory_against_the_Random_Phase_Approximation_for_the_Ethane_Dehydrogenation_Network_on_Pt_111_/24644851Test -
5دورية أكاديمية
المؤلفون: Susanne Fürst (14374014), Matthias Haasler (9254263), Robin Grotjahn (4458394), Martin Kaupp (1265817)
مصطلحات موضوعية: Biophysics, Medicine, Evolutionary Biology, Sociology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, turbomole program package, separated hybrids available, reoptimized b95c correlation, provides good balance, pig2 calibration function, d4 dispersion corrections, best local hybrids, basis set size, 2 – 3, ωlh22t performs excellently, rydberg excitation energies, range hf exchange, excitation energies, atomization energies, wide range, valence systems, valence singlet, transfer excitations, top rung, successful range, reaction barriers, range pbe
الوصف: We report the first full and efficient implementation of range-separated local hybrid functionals (RSLHs) into the TURBOMOLE program package. This enables the computation of ground-state energies and nuclear gradients as well as excitation energies. Regarding the computational effort, RSLHs scale like regular local hybrid functionals (LHs) with system or basis set size and increase timings by a factor of 2–3 in total. An advanced RSLH, ωLH22t, has been optimized for atomization energies and reaction barriers. It is an extension of the recent LH20t local hybrid and is based on short-range PBE and long-range HF exchange-energy densities, a pig2 calibration function to deal with the gauge ambiguity of exchange-energy densities, and reoptimized B95c correlation. ωLH22t has been evaluated for a wide range of ground-state and excited-state quantities. It further improves upon the already successful LH20t functional for the GMTKN55 main-group energetics test suite, and it outperforms any global hybrid while performing close to the top rung-4 functional, ωB97M-V, for these evaluations when augmented by D4 dispersion corrections. ωLH22t performs excellently for transition-metal reactivity and provides good balance between delocalization errors and left–right correlation for mixed-valence systems, with a somewhat larger bias toward localized states compared to LH20t. It approaches the accuracy of the best local hybrids to date for core, valence singlet and triplet, and Rydberg excitation energies while improving strikingly on intra- and intermolecular charge-transfer excitations, comparable to the most successful range-separated hybrids available.
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6دورية أكاديمية
المصدر: Molecules; Volume 28; Issue 9; Pages: 3834
مصطلحات موضوعية: density functional theory, water clusters, water intermolecular energy, dispersion corrections, DFT-D4
جغرافية الموضوع: agris
الوصف: Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and quantum Monte Carlo (MC) calculations, still remain. Furthermore, the application of general-purpose corrections, such as the popular Grimme’s semi-classical models (DFT-D), to different Kohn–Sham exchange–correlation functionals sometimes leads to variable and inconsistent results, which recommend a careful prior evaluation. In a recent study, we proposed a simple optimization protocol for enhancing the accuracy of these DFT-D methods by following an alternative and system-specific approach. Here, adopting the same computational strategy, we show how the accurate MC intermolecular interactions of a large set of water clusters of variable sizes (i.e., 300 (H2O)n structures, n = 9, 15, 27) can be reproduced remarkably well by dispersion-corrected DFT models (i.e., B3LYP-D4, PBE-D4, revPBE(0)-D4) upon re-optimization, reaching a mean absolute error per monomer of ~0.1 kcal/mol. Hence, the obtained results support the use of this procedure for fine-tuning tailored DFT-D models for the accurate description of targeted molecular systems.
وصف الملف: application/pdf
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7
المؤلفون: Olsson, Par A. T., Hyldgaard, Per, 1964, Schröder, Elsebeth, 1966, Jutemar, Elin Persson, Andreasson, Eskil, Kroon, Martin
المصدر: Konsistenta van der Waals täthetsfunktional-studier av bindning, struktur och optisk respons i molekylära energisystem. Föroreningspartiklars fysisorption och svaga kemisorption - atomskalig teori och beräkningar Kolbaserat höghastighet 3D GaN elektroniksystem Physical Review Materials. 2(7):7-13
مصطلحات موضوعية: dispersion corrections, Density functional theory, functionals
الوصف: We study the phase stability and martensitic transformation of orthorhombic and monoclimic polyethylene by means of density functional theory using the nonempirical consistent-exchange vdW-DF-cx functional [Phys. Rev. B 89, 035412 (2014)]. The results show that the orthorhombic phase is the most stable of the two. Owing to the occurrence of soft librational phonon modes, the monoclimic phase is predicted not to be stable at zero pressure and temperature, but becomes stable when subjected to compressive transverse deformations that pin the chains and prevent them from wiggling freely. This theoretical characterization, or prediction, is consistent with the fact that the monoclimic phase is only observed experimentally when the material is subjected to mechanical loading. Also, the estimated threshold energy for the combination of lattice deformation associated with the T1 and T2 transformation paths (between the orthorhombic and monoclimic phases) and chain shuffling is found to be sufficiently low for thermally activated back transformations to occur. Thus, our prediction is that the crystalline part can transform back from the monoclimc to the orthorhombic phase upon unloading and/or annealing, which is consistent with experimental observations. Finally, we observe how a combination of such phase transformations can lead to a fold-plane reorientation from {110} to {100} type in a single orthorhombic crystal.
وصف الملف: electronic
الوصول الحر: https://research.chalmers.se/publication/508197Test
https://research.chalmers.se/publication/504235Test
https://research.chalmers.se/publication/508197/file/508197_Fulltext.pdfTest -
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المؤلفون: Meier de Andrade, Ageo, 1990
المساهمون: Broqvist, Peter, Kullgren, Jolla, 1978, Schröder, Elsebeth, Professor
المصدر: Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology.
مصطلحات موضوعية: density functional theory, dispersion corrections, density functional analysis, transition metal, alloys, work function, lignin valorization, keto-enol tautomerization, Kemi med inriktning mot materialkemi, Chemistry with specialization in Materials Chemistry
الوصف: This thesis is built around two pillars. One is heterogeneous catalysis in the broader context of green chemistry. The focus here is on identifying catalytically active materials suitable for the valorization of renewable feedstocks. The second pillar deals with materials modelling itself, both its role to help identify the features responsible for certain desired material properties and the assessment of model quality and how to overcome challenges when modelling complex systems.Density functional theory (DFT) has become a standard method in heterogeneous catalysis and materials science, as it generally combines good accuracy with an affordable computational cost. The choice of density functional (in relation to the system under study) strongly affect the accuracy of the DFT results. In this thesis, a subset of functionals have been tested and validated with respect to their ability to predict structural and energetic properties of single- and multi-component materials. It is shown that the inclusion of dispersion corrections by computing the nonlocal correlation self-consistently, as done in the vdW-DF-cx functional, increases the accuracy of computed results in relation to experimental data. In the evaluation of the functionals, the computed properties were rationalized in terms of (i) the reduced density gradient distribution, unique for each material, and (ii) the exchange enhancement factor, unique for each density functional and dependent on the reduced density gradient distribution. Moreover, a tool is presented that can guide researchers towards the most appropriate density functional for the problem in question. This involves a protocol that brings DFT results into better agreement with experiment. Heterogeneous catalysts are complex and catalyst research is often performed using model experiments and calculations. Here descriptors have important roles to play. Two descriptors for catalytic activity have been scrutinized in this thesis. The first is the work function of metal surfaces. Here, it is shown that the adsorption of selected ad-atoms on Ni surfaces provides a route to control the metal's work function over a wide energy range. The second descriptor is the difference in stability between the enol and keto tautomers of a model lignin molecule on a model metal catalyst surface in the context of lignin depolymerization. The aim is to explore the reasons underlying the relative stabilities and to enhance the preference for enol in the keto-to-enol tautomerization. The modelling results show that a mixed PdPt alloy surface stabilizes the enol tautomer, suggesting that this could be an active catalyst for lignin depolymerization.
وصف الملف: electronic
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9
المصدر: Journal of Computer-Aided Molecular Design. 31(1):87-106
مصطلحات موضوعية: COSMO-RS, Density-functional theory, Dispersion corrections, DLPNO–CCSD(T), Host–guest systems, Ligand-binding affinities, SAMPL5, Naturvetenskap, Kemi, Teoretisk kemi, Natural Sciences, Chemical Sciences, Theoretical Chemistry
الوصف: We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO–CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by ~50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11–16 kJ/mol. DLPNO–CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates the entropy term. In conclusion, it is a challenge to calculate binding affinities for this octa-acid system with quantum–mechanical methods.
الوصول الحر: https://lup.lub.lu.se/record/ca53bb69-639b-410e-8758-706190ce3ac3Test
http://dx.doi.org/10.1007/s10822-016-9957-5Test -
10دورية أكاديمية
مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Cancer, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, three dispersion corrections, qzvpp basis sets, model species characterized, interchain dispersion interactions, dlpno – ccsd, canonical ccsd (, two functionals deviate, selected metal atoms, pex ··· pex, 25 dft functionals, polyethylene chains cross, metal atoms, chains cross, shell pex, five functionals, dft functionals, within 5, small pe3, particularly problematic, iterative triples, covalent c, cooperative effect, c bonds
الوصف: Density functional theory (DFT) functionals for calculations of binding energies (BEs) of the polyethylene (PE) chains cross-linked by selected metal atoms (M) are benchmarked against DLPNO–CCSD(T) and DLPNO–CCSD(T1) data. PEX-M-PEX complexes as compared with plain parallel PEX···PEX chains with X = 3–9 carbon atoms are model species characterized by a cooperative effect of covalent C-M-C bonds and interchain dispersion interactions. The accuracy of DLPNO–CC methods was assessed by a comparison of BEs with the canonical CCSD(T) results for small PE3-M-PE3 complexes. Functionals for PEX···PEX and closed-shell PEX-M-PEX complexes (M = Be, Mg, Zn) were benchmarked against DLPNO–CCSD(T) BEs; open-shell complexes (M = Li, Ag, Au) were benchmarked against the DLPNO–CCSD(T1) method with iterative triples. Three dispersion corrections were combined with 25 DFT functionals for calculations of BEs with respect to PEX-M and PEX fragments employing def2-TZVPP and def2-QZVPP basis sets. Accuracy to within 5% for the closed-shell PEX-M-PEX complexes was achieved with five functionals. Less accurate are functionals for the open-shell PEX-M-PEX complexes; only two functionals deviate by less than 15% from DLPNO–CCSD(T1). Particularly problematic were PEX-Li-PEX complexes. A reasonable overall performance across all complexes in terms of the mean absolute percentage error is found for the range-separated hybrid functionals ωB97X-D3 and CAM-B3LYP/D3(BJ)-ABC.
