| 1. |
- Andres, Juan, et al.
(författare)
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Nine questions on energy decomposition analysis
- 2019
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:26, s. 2248-2283
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Tidskriftsartikel (refereegranskat)abstract
- The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the “natural selection” process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the “standard model” of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another?
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| 2. |
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| 3. |
- El Bakouri, Ouissam, et al.
(författare)
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Three-Dimensional Fully π-Conjugated Macrocycles : When 3D-Aromatic and When 2D-Aromatic-in-3D?
- 2022
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:19, s. 8560-8575
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Tidskriftsartikel (refereegranskat)abstract
- Several fully π-conjugated macrocycles with puckered or cage-type structures were recently found to exhibit aromatic character according to both experiments and computations. We examine their electronic structures and put them in relation to 3D-aromatic molecules (e.g., closo-boranes) and to 2D-aromatic polycyclic aromatic hydrocarbons. Using qualitative theory combined with quantum chemical calculations, we find that the macrocycles explored hitherto should be described as 2D-aromatic with three-dimensional molecular structures (abbr. 2D-aromatic-in-3D) and not as truly 3D-aromatic. 3D-aromatic molecules have highly symmetric structures (or nearly so), leading to (at least) triply degenerate molecular orbitals, and for tetrahedral or octahedral molecules, an aromatic closed-shell electronic structure with 6n + 2 electrons. Conversely, 2D-aromatic-in-3D structures exhibit aromaticity that results from the fulfillment of Hückel’s 4n + 2 rule for each macrocyclic path, yet their π-electron counts are coincidentally 6n + 2 numbers for macrocycles with three tethers of equal lengths. It is notable that 2D-aromatic-in-3D macrocyclic cages can be aromatic with tethers of different lengths, i.e., with π-electron counts different from 6n + 2, and they are related to naphthalene. Finally, we identify tetrahedral and cubic π-conjugated molecules that fulfill the 6n + 2 rule and exhibit significant electron delocalization. Yet, their properties resemble those of analogous compounds with electron counts that differ from 6n + 2. Thus, despite the fact that these molecules show substantial π-electron delocalization, they cannot be classified as true 3D-aromatics.
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| 4. |
- Escayola, Silvia, et al.
(författare)
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Guidelines for Tuning the Excited State Huckel-Baird Hybrid Aromatic Character of Pro-Aromatic Quinoidal Compounds**
- 2021
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Ingår i: Angewandte Chemie International Edition. - : John Wiley & Sons. - 1433-7851 .- 1521-3773. ; 60:18, s. 10255-10265
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Tidskriftsartikel (refereegranskat)abstract
- Pro-aromatic molecules have higher-energy diradicaloid states that are significantly influenced by resonance structures in which conjugated rings take on Huckel-aromatic character. Recently, it has been argued that there are also pro-aromatic molecules that adopt central units with 4n pi-electron Baird-aromatic character in the T-1 state, although detailed analysis suggests that these compounds are better labelled as T-1 Huckel-Baird hybrid molecules where Huckel-aromaticity dominates. Herein, we consider a series of symmetrically substituted conjugated rings with potential Baird aromaticity in the lowest excited triplet and singlet states. Our computational results allow us to establish general guidelines for the rational design of molecules with excited state Huckel/Baird aromaticity in pro-aromatic quinoidal compounds. We found two main strategies to promote high Baird aromatic character: 1) anionic and small conjugated rings with electron donating groups as substituents and small exocyclic groups with electron withdrawing substituents, or 2) electron deficient conjugated rings with exocyclic electron-donor substitution.
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| 5. |
- Escayola, Silvia, et al.
(författare)
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In the quest of Huckel-Huckel and Huckel-Baird double aromatic tropylium (tri)cation and anion derivatives
- 2023
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Ingår i: Journal of Physical Organic Chemistry. - : John Wiley & Sons. - 0894-3230 .- 1099-1395. ; 36:1
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Tidskriftsartikel (refereegranskat)abstract
- Besides the most common form of aromaticity involving a pi-ring, hexaiodobenzene and hexakis(phenylselenyl)benzene dications also present sigma-aromaticity in the outer ring formed by the main group substituents. These two compounds are considered sigma- and pi-double aromatic, and their characterization is of special interest to the fields of organic and structural chemistry. In this work, we decided to explore the double aromaticity in substituted tropylium cations for three reasons: (i) the seven neutral halogen substituents of the tropylium cations will, without oxidation, lead to 14 sigma-electrons (a 4n + 2 Huckel number); (ii) tropylium cations are highly stable and can be easily generated experimentally; and (iii) whereas in substituted benzenes the distances between substituents in the optimized structures or X-ray crystals are too large to allow strong sigma-aromaticity, these distances are expected to be shorter in substituted tropylium cations. Yet, instead of the expected sigma-aromaticity, we found that the most stable geometries are highly puckered, meaning that delocalization in both pi- and sigma-systems is lost. Our results, which include also the tropylium anion and trication in the singlet and triplet state, show that there is a need to open a lone pair hole by oxidation to generate sigma-aromaticity. Among the systems studied, only triplet C7Br7+3 with an internal Huckel aromatic tropylium ring and an external incipient Baird aromatic Br-7 ring shows double pi- and sigma-aromaticity. This result, however, is functional-dependent and reveals that (C7Br73+)-C-3 is at the borderline for onset of double aromaticity.
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| 6. |
- Guell, Mireia, et al.
(författare)
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Theoretical study of the hydroxylation of phenolates by the Cu2O2(N,N '-dimethylethylenediamine)(2)(2+) complex
- 2009
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 14:2, s. 229-242
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Tidskriftsartikel (refereegranskat)abstract
- Tyrosinase catalyzes the ortho hydroxylation of monophenols and the subsequent oxidation of the diphenolic products to the resulting quinones. In efforts to create biomimetic copper complexes that can oxidize C-H bonds, Stack and coworkers recently reported a synthetic mu-eta(2):eta(2)-peroxodicopper(II)(DBED)(2) complex ( DBED is N,N'-di-tert-butylethylenediamine), which rapidly hydroxylates phenolates. A reactive intermediate consistent with a bis-mu-oxo-dicopper(III)-phenolate complex, with the O-O bond fully cleaved, is observed experimentally. Overall, the evidence for sequential O-O bond cleavage and C-O bond formation in this synthetic complex suggests an alternative mechanism to the concerted or late-stage O-O bond scission generally accepted for the phenol hydroxylation reaction performed by tyrosinase. In this work, the reaction mechanism of this peroxodicopper(II) complex was studied with hybrid density functional methods by replacing DBED in the mu-eta(2):eta(2)-peroxodicopper(II)(DBED)(2) complex by N,N'-dimethylethylenediamine ligands to reduce the computational costs. The reaction mechanism obtained is compared with the existing proposals for the catalytic ortho hydroxylation of monophenol and the subsequent oxidation of the diphenolic product to the resulting quinone with the aim of gaining some understanding about the copper-promoted oxidation processes mediated by 2: 1 Cu(I)O-2-derived species.
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| 7. |
- Guell, Mireia, et al.
(författare)
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Theoretical study of the hydroxylation of phenols mediated by an end-on bound superoxo-copper(II) complex
- 2009
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 14:2, s. 273-285
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Tidskriftsartikel (refereegranskat)abstract
- Peptidylglycine alpha-amidating monooxygenase and dopamine beta-monooxygenase are copper-containing proteins which catalyze essential hydroxylation reactions in biological systems. There are several possible mechanisms for the reductive O-2-activation at their mononuclear copper active site. Recently, Karlin and coworkers reported on the reactivity of a copper(II)-superoxo complex which is capable of inducing the hydroxylation of phenols with incorporated oxygen atoms derived from the Cu(II)-O-2(-) moiety. In the present work the reaction mechanism for the abovementioned superoxo complex with phenols is studied. The pathways found are analyzed with the aim of providing some insight into the nature of the chemical and biological copper-promoted oxidative processes with 1:1 Cu(I)/O-2-derived species.
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| 8. |
- Jimenez-Halla, J. Oscar C., et al.
(författare)
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Organomagnesium clusters : Structure, stability, and bonding in archetypal models
- 2011
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Ingår i: Journal of Organometallic Chemistry. - : Elsevier BV. - 0022-328X .- 1872-8561. ; 696:25, s. 4104-4111
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the molecular structure and the nature of the chemical bond in the monomers and tetramers of the Grignard reagent CH(3)MgCl as well as MgX(2) (X = H, Cl, and CH(3)) at the BP86/TZ2P level of theory. For the tetramers, we discuss the stability of three possible molecular structures of C(2h), D(2h), and T(d) symmetry. The most stable structure for (MgCl(2))(4) is D(2h), the one for (MgH(2))(4) is C(2h), and that of (CH(3)MgCl)(4) is T(d). The latter is 38 kcal/mol more stable with chlorines in bridge positions and methyl groups coordinated to a Mg vertex than vice versa. We find through a quantitative energy decomposition analysis (EDA) that the tetramerization energy is predominantly composed of electrostatic attraction Delta V(elstat) (60% of all bonding terms Delta V(elstat) + Delta E(oi)) although the orbital interaction Delta E(oi) also provides an important contribution (40%).
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| 9. |
- López-Villellas, Lorién, et al.
(författare)
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Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code
- 2023
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Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 288
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Tidskriftsartikel (refereegranskat)abstract
- In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton’s method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers.
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| 10. |
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