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It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional. 相似文献
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12 not so angry men: Hexaphenylethane is unstable, a phenomenon traditionally attributed to steric repulsion between the six phenyl rings. However, adding 12 bulky tert-butyl groups, one to each of the 12 meta positions, gives a stabile ethane derivative (see space-filling model and potential energy curve for the dissociation of the central C-C bond). This unexpected stabilization is shown to result from attractive dispersion interactions between the substituents. 相似文献
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《International journal of quantum chemistry》2018,118(16)
CCSD(T)/CBS and DFT methods are employed to study the stacking interactions of acetylacetonate‐type (acac‐type) chelates of nickel, palladium, and platinum with benzene. The strongest chelate–aryl stacking interactions are formed by nickel and palladium chelate, with interaction energies of −5.75 kcal mol−1 and −5.73 kcal mol−1, while the interaction of platinum chelate is weaker, with interaction energy of −5.36 kcal mol−1. These interaction energies are significantly stronger than stacking of two benzenes, −2.73 kcal mol−1. The strongest nickel and palladium chelate–aryl interactions are with benzene center above the metal area, while the strongest platinum chelate–aryl interaction is with the benzene center above the C2 atom of the acac‐type chelate ring. These preferences arise from very different electrostatic potentials above the metal ions, ranging from very positive above nickel to slightly negative above platinum. While the differences in electrostatic potentials above metal atoms cause different geometries with the most stable interaction among the three metals, the dispersion (correlation energy) component is the largest contribution to the total interaction energy for all three metals. 相似文献
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Markus Bursch Lukas Kunze Dr. Amol M. Vibhute Dr. Andreas Hansen Prof. Dr. Kana M. Sureshan Dr. Peter G. Jones Prof. Dr. Stefan Grimme Prof. Dr. Daniel B. Werz 《Chemistry (Weinheim an der Bergstrasse, Germany)》2021,27(14):4627-4639
The noncovalent interactions between azides and oxygen-containing moieties are investigated through a computational study based on experimental findings. The targeted synthesis of organic compounds with close intramolecular azide–oxygen contacts yielded six new representatives, for which X-ray structures were determined. Two of those compounds were investigated with respect to their potential conformations in the gas phase and a possible significantly shorter azide–oxygen contact. Furthermore, a set of 44 high-quality, gas-phase computational model systems with intermolecular azide–pnictogen (N, P, As, Sb), –chalcogen (O, S, Se, Te), and –halogen (F, Cl, Br, I) contacts are compiled and investigated through semiempirical quantum mechanical methods, density functional approximations, and wave function theory. A local energy decomposition (LED) analysis is applied to study the nature of the noncovalent interaction. The special role of electrostatic and London dispersion interactions is discussed in detail. London dispersion is identified as a dominant factor of the azide–donor interaction with mean London dispersion energy-interaction energy ratios of 1.3. Electrostatic contributions enhance the azide–donor coordination motif. The association energies range from −1.00 to −5.5 kcal mol−1. 相似文献
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De la Pierre M Orlando R Maschio L Doll K Ugliengo P Dovesi R 《Journal of computational chemistry》2011,32(9):1775-1784
The performance of six different density functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in describing the infrared spectrum of forsterite, a crystalline periodic system with orthorhombic unit cell (28 atoms in the primitive cell, Pbmn space group), is investigated by using the periodic ab initio CRYSTAL09 code and an all‐electron Gaussian‐type basis set. The transverse optical (TO) branches of the 35 IR active modes are evaluated at the equilibrium geometry together with the oscillator strengths and the high‐frequency dielectric tensor ?∞. These quantities are essential to compute the dielectric function ?(ν), and then the reflectance spectrum R(ν), which is compared with experiment. It turns out that hybrid functionals perform better than LDA and GGA, in general; that B3LYP overperforms WC1LYP and, in turn, PBE0; that PBESOL is better than PBE; that LDA is the worst performing functional among the six under study. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 相似文献
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Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition schemes. In polar interactions such as hydrogen bonds, it can contribute ten or several tens of percent of the interaction energy. Less is known about its importance in higher-order interactions in many-body systems, mainly because of the lack of methods applicable to this problem. In this work, we extend our method for the quantification of the charge-transfer energy based on constrained DFT to many-body cases and apply it to model trimers extracted from molecular crystals. Our calculations show that charge transfer can account for a large fraction of the total three-body interaction energy. This also has implications for DFT calculations of many-body interactions in general as it is known that many DFT functionals struggle to describe charge-transfer effects correctly. 相似文献
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Previously, we introduced DFT-D3(BJ)ω B97X-V and ω B97M-V functionals and assessed them for the GMTKN55 database [Najibi and Goerigk, J Chem. Theory Comput. 2018, 14, 5725]. In this study, we present DFT-D4 damping parameters to build the DFT-D4 counterparts of these functionals and assess these in comparison. We extend our analysis beyond GMTKN55 and especially turn our attention to enzymatically catalyzed and metal–organic reactions. We find that B97M-D4 is now the second-best performing meta-generalized-gradient approximation functional for the GMTKN55 database and it can provide noticeably better organometallic reaction energies compared to B97M-D3(BJ). Moreover, the aforementioned DFT-D3(BJ)-based functionals have not been thoroughly assessed for geometries and herein we close this gap by analyzing geometries of noncovalently bound dimers and trimers, peptide conformers, water hexamers and transition-metal complexes. We find that several of the B97(M)-based methods—particularly the DFT-D4 versions—surpass the accuracy of previously studied methods for peptide conformer, water hexamer, and transition-metal complex geometries, making them safe-to-use, cost-efficient alternatives to the original methods. The DFT-D4 variants can be easily used with ORCA4.1 and above. 相似文献
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Cover Picture: Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials (Chem. Eur. J. 17/2014)
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Dr. Mercedes Alonso Tatiana Woller Dr. Francisco J. Martín‐Martínez Dr. Julia Contreras‐García Prof. Paul Geerlings Prof. Frank De Proft 《Chemistry (Weinheim an der Bergstrasse, Germany)》2014,20(17):4841-4841
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Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials
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Dr. Mercedes Alonso Tatiana Woller Dr. Francisco J. Martín‐Martínez Dr. Julia Contreras‐García Prof. Paul Geerlings Prof. Frank De Proft 《Chemistry (Weinheim an der Bergstrasse, Germany)》2014,20(17):4931-4941
Noncovalent interactions involving aromatic rings, such as π‐stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion‐corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene???methane and cyclohexane???methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel‐displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non‐additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials. 相似文献
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Computational study of ground-state properties of μ2-bridged group 14 porphyrinic sandwich complexes
Julia Kohn Markus Bursch Andreas Hansen Stefan Grimme 《Journal of computational chemistry》2023,44(3):229-239
The structural properties of μ2-bridged porphyrinic double-decker complexes are investigated and the influence of various ligands, metals, substituents, and bridging atoms on the dominant structural motif is elucidated. A variety of quantum chemical methods including semiempirical (SQM) methods and density functional theory (DFT) is assessed for the calculation of ecliptic and staggered conformational energies. Local coupled cluster (DLPNO-CCSD(T1)) data are generated for reference. The r2SCAN-3c composite scheme as well as the B2PLYP-D4/def2-QZVPP approach are identified as reliable methods. Energy decomposition analyses (EDA) and localized molecular orbital analyses (LMO) are used to investigate the bonding situation and the nature of the inter-ligand interaction energy underlining the crucial role of attractive London dispersion interactions. Targeted modification of the bridging atom, e.g., by replacing O2− by S2− is shown to drastically change the major structural features of the investigated complexes. Further, the influence of different substituents of varying size at the phthalocyanine ligand regarding the dominant conformation is described. 相似文献
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Dr. Patrick M. J. Szell Zainab Rehman Ben P. Tatman Dr. Leslie P. Hughes Dr. Helen Blade Prof. Steven P. Brown 《Chemphyschem》2023,24(3):e202200558
Crystallographic disorder, whether static or dynamic, can be detrimental to the physical and chemical stability, ease of crystallization and dissolution rate of an active pharmaceutical ingredient. Disorder can result in a loss of manufacturing control leading to batch-to-batch variability and can lengthen the process of structural characterization. The range of NMR active nuclei makes solid-state NMR a unique technique for gaining nucleus-specific information about crystallographic disorder. Here, we explore the use of high-field 35Cl solid-state NMR at 23.5 T to characterize both static and dynamic crystallographic disorder: specifically, dynamic disorder occurring in duloxetine hydrochloride ( 1 ), static disorder in promethazine hydrochloride ( 2 ), and trifluoperazine dihydrochloride ( 3 ). In all structures, the presence of crystallographic disorder was confirmed by 13C cross-polarization magic-angle spinning (CPMAS) NMR and supported by GIPAW-DFT calculations, and in the case of 3 , 1H solid-state NMR provided additional confirmation. Applying 35Cl solid-state NMR to these compounds, we show that higher magnetic fields are beneficial for resolving the crystallographic disorder in 1 and 3 , while broad spectral features were observed in 2 even at higher fields. Combining the data obtained from 1H, 13C, and 35Cl NMR, we show that 3 exhibits a unique case of disorder involving the +N−H hydrogen positions of the piperazinium ring, driving the chloride anions to occupy three distinct sites. 相似文献
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Ana Maria Toader Maria Cristina Buta Alice Mischie Mihai V. Putz Fanica Cimpoesu 《Molecules (Basel, Switzerland)》2022,27(1)
Aromatic hydrocarbons with fused benzene rings and regular triangular shapes, called n-triangulenes according to the number of rings on one edge, form groundstates with n-1 unpaired spins because of topological reasons. Here, we focus on methodological aspects emerging from the density functional theory (DFT) treatments of dimer models of the n = 2 triangulene (called also phenalenyl), observing that it poses interesting new problems to the issue of long-range corrections. Namely, the interaction comprises simultaneous spincoupling and van der Waals effects, i.e., a technical conjuncture not considered explicitly in the benchmarks calibrating long-range corrections for the DFT account of supramolecular systems. The academic side of considering dimer models for calculations and related analysis is well mirrored in experimental aspects, and synthetic literature revealed many compounds consisting of stacked phenalenyl cores, with intriguing properties, assignable to their long-range spin coupling. Thus, one may speculate that a thorough study assessing the performance of state-of-the-art DFT procedures has relevance for potential applications in spintronics based on organic compounds. 相似文献
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The mechanism of a cycloaddition reaction between singlet dichloromethylene germylene and ethylene has been investigated with B3LYP/6-31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD(T)//B3LYP/6-31G* method. On the basis of the surface energy profile obtained with CCSD(T)// B3LYP/6-31G* method for the cycloaddition reaction between singlet dichloromethylene germylene and ethylene, it can be predicted that the dominant reaction pathway is that an intermediate INT1 is firstly formed between the two reactants through a barrier-free exothermic reaction of 61.7 kJ/mol, and the intermediate INT1 then isomerizes to an active four-membered ring product P2.1 via a transition state TS2, an intermediate INT2 and a transition state TS2.1, in which energy barriers are 57.7 and 42.2 kJ/mol, respectively. 相似文献
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The binding of two metal ions that are in close proximity in proteins is examined using a combination of (1) crystallographic structural database analyses and (2) density functional theory calculations on model complexes. Divalent magnesium and manganese ions are the focus of the present study. It is found that in all proteins in the Protein Databank that have two closely positioned magnesium or manganese ions, these metal ions are generally bridged by at least one negatively charged oxygen-containing group—carboxylate, phosphate, or sulfate. This group transfers (negative) electron density to the metal ions and this helps to reduce electrostatic repulsion in the region. The geometry of the two-metal complex appears to depend on the nature of the negatively charged group between them. When a single oxygen atom is also in a bridging position, the two metal ions are found to be closer together than when only a carboxylate group binds them together. This suggests that this bridging oxygen atom may be negatively charged, e.g., a hydroxide ion rather than a water molecule. Details of the geometry of such bridges and the relevant motifs that are found in crystal structures are described. 相似文献
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Density functional theory (DFT) B3LYP method is used to theoretically investigate the adsorption conformations of H2O and glycol on the relaxation surface of β-Si3N4(0001) with cluster models. For H2O, the most stable structure is that adsorbed through the H atom lying above a N(3) site of the relaxation surface of β-Si3N4(0001); while for glycol, it is the one adsorbed via the H atom lying above the center of Si(2) and N(3) of the same relaxation surface. The adsorption energy, adsorption bond and transfer electrons of the two adsorbed substances prove that glycol is easy to be adsorbed on the relaxation surface of β-Si3N4(0001). 相似文献
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Li Ping Cheng Jing Li Wang Ying Xin Sun 《International journal of quantum chemistry》2015,115(2):68-76
Density functional theory method is used to examine a series of group III triazides X(N3)3 (X = B, Al, Ga). These compounds, except for the C3h planar B(N3)3 and Al(N3)3, are first reported here. C3h planar structures are the most energetically favored for all singlet X(N3)3 systems. Potential‐energy surfaces for unimolecular decompositions of the C3h and CS planar X(N3)3 species have been investigated. Results show that decomposition of B(N3)3 obeys sequential fashion and follows a four‐step mechanism: (1) B(N3)3 → NB(N3)2 + N2; (2) NB(N3)2 → cyc‐N2BN3 + N2; (3) cyc‐N2BN3 → trigonal‐BN3 + N2; (4) trigonal‐BN3 → linear‐NBNN. Decomposition of Al(N3)3 follows a two‐step mechanism: (1) Al(N3)3 → NAl(N3)2 + N2; (2) NAl(N3)2 → linear‐AlN3 + 2N2. The dissociation of Ga(N3)3 follows only one‐step mechanism: Ga(N3)3 → angular‐GaN3 + 3N2. These findings may be helpful in understanding the decomposition mechanisms of group III triazides as well as the possible mechanism for XN film generation. © 2014 Wiley Periodicals, Inc. 相似文献
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Werner Reckien Florian Janetzko Michael F. Peintinger Thomas Bredow 《Journal of computational chemistry》2012,33(25):2023-2031
A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT‐D3) is implemented in the plane‐wave program package VASP. The DFT‐D3 implementation is compared with an implementation of the earlier DFT‐D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT‐D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three‐center terms as implemented in the original molecular DFT‐D3 version is investigated. The empirical parameters are taken from the original DFT‐D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid‐state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT‐D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106). © 2012 Wiley Periodicals, Inc. 相似文献
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Yuichiro Yoshida Hayato Yokoi Hirofumi Sato 《Journal of computational chemistry》2020,41(26):2240-2250
A bird's-eye view of the water splitting and H2 generation at a ruthenium(II) pincer complex is presented. Using a combination of density functional theory and efficient algorithms for exploration of potential energy hypersurface (PES), a total of 197 local minima and 186 transition states are identified, and a new mechanism for water splitting and H2 evolution via hydroxycarbonyl intermediates is presented. Furthermore, a global feature of the reaction PES, so-called potential energy landscape, is discussed on analyzing the obtained structures. As a result, the landscape is characterized by hierarchical structure, namely, PES consists of many “superbasins (SBs)” that are separated by relatively high energy barriers corresponding to bond breaking around Ru(II) center. Each SB involves a set of conformational isomers that can be interchanged with each other through relatively small barriers. To the best of our best knowledge, this is the first report on the quantum chemical computation of the hierarchical structure of PES for a realistic, catalytic reaction system. 相似文献