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1.
J Phys Chem B ; 2020 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-32633534

RESUMO

An efficient approach for an accurate quantum mechanical (QM) modeling of infrared (IR) spectra of condensed-phase systems is described. An ensemble of energetically low-lying cluster structures of a solute molecule surrounded by an explicit shell of solvent molecules is efficiently generated at the semiempirical tight-binding QM level and then reoptimized at the density functional theory level of theory. The IR spectrum of the solvated molecule is obtained as a thermodynamic average of harmonically computed QM spectra for all significantly populated cluster structures. The accuracy of such simulations in comparison to experimental data for some organic compounds and their solutions is shown to be the same or even better than the corresponding QM computations of the gas-phase IR spectrum for the isolated molecule.

2.
Artigo em Inglês | MEDLINE | ID: mdl-32484309

RESUMO

The exhaustive trichlorosilylation of hexachloro-1,3-butadiene was achieved in one step by using a mixture of Si2 Cl6 and [nBu4 N]Cl (7:2 equiv) as the silylation reagent. The corresponding butadiene dianion salt [nBu4 N]2 [1] was isolated in 36 % yield after recrystallization. The negative charges of [1]2- are mainly delocalized across its two carbanionic (Cl3 Si)2 C termini (α-effect of silicon) such that the central bond possesses largely C=C double-bond character. Upon treatment with 4 equiv of HCl, [1]2- is converted into neutral 1,2,3,4-tetrakis(trichlorosilyl)but-2-ene, 3. The Cl- acceptor AlCl3 , induces a twofold ring-closure reaction of [1]2- to form a six-membered bicycle 4 in which two silacyclobutene rings are fused along a shared C=C double bond (84 %). Compound 4, which was structurally characterized by X-ray crystallography, undergoes partial ring opening to a monocyclic silacyclobutene 2 in the presence of HCl, but is thermally stable up to at least 180 °C.

3.
J Am Chem Soc ; 142(25): 11072-11083, 2020 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-32464052

RESUMO

A highly modular synthesis of BNB- and BOB-doped phenalenyls is presented. Treatment of the 1,8-naphthalenediyl-bridged boronic acid anhydride 1 with LiAlH4/Me3SiCl afforded the corresponding 1,8-naphthalenediyl-supported diborane(6) 2, which served as the starting material for all subsequent transformations. Upon addition of MesMgBr/Me3SiCl, 2 was readily converted to the tetraorganyl diborane(6) 5. The further heteroatoms were finally introduced through the reaction of 2 with (Me3Si)2NR' or 5 with H2NR' or H2O (R' = H, Me, p-Tol). A helically twisted, fully BNB-embedded PAH 11 was prepared by combining 2 with a dibrominated m-terphenylamine, followed by a Grignard-mediated double ring-closure reaction. All compounds devoid of B-H bonds show favorable optoelectronic properties, such as luminescence and reversible reduction behavior. In the case of the BNB-phenalenyl 7 (BMes, NMe), the radical-anion salt K[7•] was generated through chemical reduction with K metal and characterized by EPR spectroscopy. K[7•] is not long-term stable in a THF/c-hexane solution, but abstracts an H atom with formation of the diamagnetic BNB-doped 1H-phenalene K[7H].

4.
J Chem Phys ; 152(16): 164303, 2020 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-32357787

RESUMO

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.

5.
J Phys Chem B ; 124(18): 3636-3646, 2020 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-32275425

RESUMO

Special-purpose classical force fields (FFs) provide good accuracy at very low computational cost, but their application is limited to systems for which potential energy functions are available. This excludes most metal-containing proteins or those containing cofactors. In contrast, the GFN2-xTB semiempirical quantum chemical method is parametrized for almost the entire periodic table. The accuracy of GFN2-xTB is assessed for protein structures with respect to experimental X-ray data. Furthermore, the results are compared with those of two special-purpose FFs, HF-3c, PM6-D3H4X, and PM7. The test sets include proteins without any prosthetic groups as well as metalloproteins. Crystal packing effects are examined for a set of smaller proteins to validate the molecular approach. For the proteins without prosthetic groups, the special purpose FF OPLS-2005 yields the smallest overall RMSD to the X-ray data but GFN2-xTB provides similarly good structures with even better bond-length distributions. For the metalloproteins with up to 5000 atoms, a good overall structural agreement is obtained with GFN2-xTB. The full geometry optimizations of protein structures with on average 1000 atoms in wall-times below 1 day establishes the GFN2-xTB method as a versatile tool for the computational treatment of various biomolecules with a good accuracy/computational cost ratio.

6.
Artigo em Inglês | MEDLINE | ID: mdl-32343883

RESUMO

Modern chemistry seems to be unlimited in molecular size and elemental composition. Metal-organic frameworks or biological macromolecules involve complex architectures and a large variety of elements. Yet, a general and broadly applicable theoretical method to describe the structures and interactions of molecules beyond the 1000-atom size regime semi-quantitatively is not self-evident. For this purpose, a generic force field named GFN-FF is presented, which is completely newly developed to enable fast structure optimizations and molecular-dynamics simulations for basically any chemical structure consisting of elements up to radon. The freely available computer program requires only starting coordinates and elemental composition as input from which, fully automatically, all potential-energy terms are constructed. GFN-FF outperforms other force fields in terms of generality and accuracy, approaching the performance of much more elaborate quantum-mechanical methods in many cases.

7.
Phys Chem Chem Phys ; 2020 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-32292979

RESUMO

We present an extension of the DFT-D4 model [J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredients are additional reference polarizabilities for highly-coordinated group 1-5 elements derived from pseudo-periodic electrostatically-embedded cluster calculations. To illustrate the performance of the updated method, several test cases are considered, for which we compare D4 to its predecessor D3(BJ), as well as to a comprehensive set of other dispersion-corrected methods. The largest improvements are observed for solid-state polarizabilities of 16 inorganic salts, where the D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides values in good agreement with experimental and/or high-level references. These results suggest the application of the proposed D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.

8.
J Am Chem Soc ; 142(19): 8763-8775, 2020 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-32279489

RESUMO

Porous molecular materials combine benefits such as convenient processability and the possibility for atom-precise structural fine-tuning which makes them remarkable candidates for specialty applications in the areas of gas separation, catalysis, and sensing. In order to realize the full potential of these materials and guide future molecular design, knowledge of the transition from molecular properties into materials behavior is essential. In this work, the class of compounds termed cycloparaphenylenes (CPPs)-shape-persistent macrocycles with built-in cavities and radially oriented π-systems-was selected as a conceptually simple class of intrinsically porous nanocarbons to serve as a platform for studying the transition from analyte sorption properties of small aggregates to those of bulk materials. In our detailed investigation, two series of CPPs were probed: previously reported hoop-shaped [n]CPPs and a novel family of all-phenylene figure-8 shaped (lemniscal) bismacrocycles, termed spiro[n,n]CPPs. A series of nanocarbons with different macrocycle sizes and heteroatom content have been prepared by atom-precise organic synthetic methods, and their structural, photophysical, and electronic attributes were disclosed. Detailed experimental studies (X-ray crystallography, gas sorption, and quartz-crystal microbalance measurements) and quantum chemical calculations provided ample evidence for the importance of the solid-state arrangement on the porosity and analyte uptake ability of intrinsically porous molecular nanocarbons. We demonstrate that this molecular design principle, i.e., incorporation of sterically demanding spiro junctions into the backbone of nanohoops, enables the manipulation of solid-state morphology without significantly changing the nature and size of the macrocyclic cavities. As a result, the novel spiro[n,n]CPPs showed a remarkable performance as high affinity material for vapor analyte sensing.

9.
J Phys Chem B ; 124(13): 2568-2578, 2020 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-32148035

RESUMO

Peptide chains can model endogenous biotags for applications in second-harmonic imaging microscopy. Such structures are flexible which may strongly affect their structure-property relationship. Here, we explore quantum-mechanically the conformational space of a set of tryptophan-rich model peptides. This has become feasible because of the recently proposed meta-dynamics method based on efficient tight-binding (TB) calculations. The TB version of the simplified time-dependent density functional theory (sTD-DFT-xTB) method is used to evaluate the first hyperpolarizability (ß). These new tools enable us to calculate nonlinear optical properties for systems with several thousand atoms and/or to screen large structure ensembles. First, we show that the indole chromophore in tryptophan residues dominates the ß response of these systems. Their relative orientation mostly determines the global ß tensor and affects the static ß response. The results underline the importance of finding low-energy conformers for modeling ß of flexible molecules. Additionally, we compare calculated and extrapolated experimental static ß. The sTD-DFT-xTB method is capable of providing reliable second-harmonic generation values for tryptophan-rich systems at a fraction of the computational cost of the commonly used TD-DFT/TD-HF levels of theory.

10.
J Chem Theory Comput ; 16(3): 2002-2012, 2020 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-32074450

RESUMO

We present an efficient computational protocol for robust transition state localization that can be routinely applied to complex (organometallic) reactions. The capabilities of the combination of extended tight-binding semiempirical methods (GFNn-xTB) with a state-of-the-art transition state localization algorithm (mGSM) is demonstrated on a modified version of the MOBH35 benchmark set, consisting of 29 organometallic reactions and transition states. Furthermore, for three examples we demonstrate how error-prone the conventional (manual) approach based on chemical intuition can be and how errors are avoided by a semiautomated generation of reaction profiles. The performance of the GFNn-xTB methods is carefully assessed and compared with that of the widely used PM6-D3H4 and PM7 semiempirical methods. The GFNn-xTB methods show much higher success rates of 89.7% (GFN1-xTB) and 86.2% (GFN2-xTB) compared with 72.4% for PM6-D3H4 and 69.0% for PM7. The barrier heights and reaction energies are computed with much better accuracy at reduced computational cost for the GFNn-xTB methods compared with the PMx methods, allowing a semiquantitative assessment of possible reaction pathways already at a semiempirical level. The mean error of GFN2-xTB for the barrier heights (8.2 kcal mol-1) is close to what low-cost density functional approximations provide and substantially smaller than the corresponding error of the competitor methods.

11.
Phys Chem Chem Phys ; 22(14): 7169-7192, 2020 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-32073075

RESUMO

We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.

12.
Chemistry ; 26(15): 3335-3347, 2020 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-31815311

RESUMO

Two isostructural ligands with either nitrile (Lnit ) or isonitrile (Liso ) moieties directly connected to a [2.2]paracyclophane backbone with pseudo-meta substitution pattern have been synthesized. The ligand itself (Lnit ) or its precursors (Liso ) were resolved by HPLC on a chiral stationary phase and the absolute configuration of the isolated enantiomers was assigned by XRD analysis and/or by comparison of quantum-chemical simulated and experimental electronic circular dichroism (ECD) spectra. Surprisingly, the resulting metallosupramolecular aggregates formed in solution upon coordination of [(dppp)Pd(OTf)2 ] differ in their composition: whereas Lnit forms dinuclear complexes, Liso exclusively forms trinuclear ones. Furthermore, they also differ in their chiral self-sorting behavior as (rac)-Liso undergoes exclusive social self-sorting leading to a heterochiral assembly, whereas (rac)-Liso shows a twofold preference for the formation of homochiral complexes in a narcissistic self-sorting manner as proven by ESI mass spectrometry and NMR spectroscopy. Interestingly, upon crystallization, these discrete aggregates undergo structural transformation to coordination polymers, as evidenced by single-crystal X-ray diffraction.

13.
Angew Chem Int Ed Engl ; 59(13): 5102-5107, 2020 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-31793163

RESUMO

Heterobifunctional rotaxanes serve as efficient catalysts for the addition of malonates to Michael acceptors. We report a series of four different heterobifunctional rotaxanes, featuring an amine-based thread and a chiral 1,1'-binaphthyl-phosphoric-acid-based macrocycle. High-level DFT calculations provided mechanistic insights and enabled rational catalyst improvements, leading to interlocked catalysts that surpass their non-interlocked counterparts in terms of reaction rates and stereoselectivities.

14.
J Phys Chem A ; 123(45): 9828-9839, 2019 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-31633918

RESUMO

Polycyclic hydrocarbons are often used to understand the electronic structure of nanographene systems. Among them, indeno[1,2b]fluorene and indeno[1,2c]fluorene isomers present a central p-quinodimethane unit leading to unique optical properties. In this work, we characterized the absorption spectra of indeno[1,2b]fluorene and [2,1-c]diindeno[n]thiophene derivatives with (spin-flip) simplified time-dependent density functional theory [(SF-)sTD-DFT] methods. Note that the SF-sTD-DFT level of theory allows a computationally efficient treatment for large diradicals. To interpret spectra, we implemented natural transition orbitals (NTOs) at both SF-sTD-DFT and sTD-DFT levels. This compact and method-independent representation of the electronic excitation provides a simple interpretation for the low-lying excited states of this set of molecules in terms of three different types of NTOs: "quinoid", "aromatic", and "π-bonded". When comparing with experiment, we found that only one molecule of this set is actually a high-spin triplet diradical. Others are almost closed-shell molecules with a very small contribution from a doubly excited configuration that only the spin-flip method could capture. The small amount of static correlation recovered by the spin-flip active space provides a linear relation between the first visible theoretical and experimental excitation energies among this set.

15.
Angew Chem Int Ed Engl ; 58(48): 17307-17311, 2019 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-31566863

RESUMO

A metal-free, intermolecular syn-addition of hexamethyldisilane across simple alkenes is reported. The catalytic cycle is initiated and propagated by the transfer of a methyl group from the disilane to a silylium-ion-like intermediate, corresponding to the (re)generation of the silylium-ion catalyst. The key feature of the reaction sequence is the cleavage of the Si-Si bond in a 1,3-silyl shift from silicon to carbon. A central intermediate of the catalysis was structurally characterized by X-ray diffraction, and the computed reaction mechanism is fully consistent with the experimental findings.

16.
ACS Omega ; 4(12): 15120-15133, 2019 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-31552357

RESUMO

In this work, we have tested two different extended tight-binding methods in the framework of the quantum chemistry electron ionization mass spectrometry (QCEIMS) program to calculate electron ionization mass spectra. The QCEIMS approach provides reasonable, first-principles computed spectra, which can be directly compared to experiment. Furthermore, it provides detailed insight into the reaction mechanisms of mass spectrometry experiments. It sheds light upon the complicated fragmentation procedures of bond breakage and structural rearrangements that are difficult to derive otherwise. The required accuracy and computational demands for successful reproduction of a mass spectrum in relation to the underlying quantum chemical method are discussed. To validate the new GFN2-xTB approach, we conduct simulations for 15 organic, transition-metal, and main-group inorganic systems. Major fragmentation patterns are analyzed, and the entire calculated spectra are directly compared to experimental data taken from the literature. We discuss the computational costs and the robustness (outliers) of several calculation protocols presented. Overall, the new, theoretically more sophisticated semiempirical method GFN2-xTB performs well and robustly for a wide range of organic, inorganic, and organometallic systems.

17.
Chemistry ; 25(63): 14388-14398, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31386227

RESUMO

Pulsed electron paramagnetic resonance (EPR) dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling constants and thus the distance between electron spin centers. Up to now, PDS measurements have been mostly applied to spin centers whose g-anisotropies are moderate and therefore have a negligible effect on the dipolar coupling constants. In contrast, spin centers with large g-anisotropy yield dipolar coupling constants that depend on the g-values. In this case, the usual methods of extracting distances from the raw PDS data cannot be applied. Here, the effect of the g-anisotropy on PDS data is studied in detail on the example of the low-spin Fe3+ ion. First, this effect is described theoretically, using the work of Bedilo and Maryasov (Appl. Magn. Reson. 2006, 30, 683-702) as a basis. Then, two known Fe3+ /nitroxide compounds and one new Fe3+ /trityl compound were synthesized and PDS measurements were carried out on them using a method called relaxation induced dipolar modulation enhancement (RIDME). Based on the theoretical results, a RIDME data analysis procedure was developed, which facilitated the extraction of the inter-spin distance and the orientation of the inter-spin vector relative to the Fe3+ g-tensor frame from the RIDME data. The accuracy of the determined distances and orientations was confirmed by comparison with MD simulations. This method can thus be applied to the highly relevant class of metalloproteins with, for example, low-spin Fe3+ ions.

18.
J Am Chem Soc ; 141(36): 14370-14383, 2019 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-31390863

RESUMO

A series of formally triply bonded diplumbyne analogues of alkynes of the general formula ArPbPbAr (Ar = terphenyl ligand with different steric properties) was synthesized by two routes. All diplumbyne products were synthesized by a simple reduction of the corresponding Pb(II) halide precursor ArPb(Br) by DIBAL-H with yields in the range 8-48%. For one of the diplumbynes ArPri4PbPbArPri4 (ArPri4 = C6H3-2,6-(C6H3-2,6-Pri2)2) it was shown that reduction of ArPri4Pb(Br) using a magnesium(I) beta-diketiminate afforded a much improved yield in comparison (29 vs 8%) to that obtained by reduction with DIBAL-H. The more sterically crowded diplumbyne ArPri8PbPbArPri8 (ArPri8 = C6H-3,5-Pri2-2,6-(C6H2-2,4,6-Pri3)2) displayed a shortened Pb-Pb bond with a length of 3.0382(5) Å and wide Pb-Pb-C angles of 114.73(7)° and 116.02(6)° consistent with multiple-bond character with a bond order of up to 1.5. The others displayed longer metal-metal distances and narrower Pb-Pb-C angles that were consistent with a lower bond order that approached one. Computational studies of the diplumbynes yielded detailed insight of the unusual bonding and explained their similar electronic spectra arising from the flexibility of the C-Pb-Pb-C core in solution. Furthermore, the importance of London dispersion interactions for the stabilization of the diplumbynes was demonstrated.

19.
ChemistryOpen ; 8(6): 807-810, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31293872

RESUMO

Extensive DFT calculations provide deep mechanistic insights into the acylation reactions of tert-butyl dibenzo-7-phosphanobornadiene with PhCOX (X=Cl, Br, I, OTf) in CH2Cl2 solution. Such reactions are initialized by the nucleophilic P⋅⋅⋅C attack to the carbonyl group to form the acylphosphonium intermediate A+ together with X- anion, followed either by nucleophilic X-⋅⋅⋅P attack (X=Cl, Br, and I) toward A+ to eliminate anthracene or by slow rearrangement or decomposition of A+ (X=OTf). In contrast to the first case (X=Cl) that is rate-limited by the initial P⋅⋅⋅C attack, other reactions are rate-limited by the second X-⋅⋅⋅P attack for X=Br and I and even thermodynamically prevented for X=OTf, leading to isolable phosphonium salts. The rearrangement of phosphonium A+ is initiated by a P-C bond cleavage, followed either by sequential proton-shifts to form anthracenyl acylphosphonium or by deprotonation with additional base Et3N to form neutral anthracenyl acylphosphine. Our DFT results strongly support the separated acylphosphonium A+ as the key reaction intermediate that may be useful for the transfer of acylphosphenium in general.

20.
Phys Chem Chem Phys ; 21(33): 18048-18058, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31219481

RESUMO

The design, implementation, and evaluation of a computationally efficient approach for exploring the chemical nature and bulk properties of the super-heavy main-group elements (SHEs) Cn-Og with nuclear charges of Z = 112-118 is described. The approach combines plane-wave density-functional theory (DFT) based on a newly devised set of projector-augmented wave potentials (PAWs) with the D3 dispersion correction, whose parameter-space is extended for this purpose. Regarding both, the fitting of the PAWs as well as the calculation of the D3 parameters, it is shown that the peculiar electronic structure of the SHEs with strong relativistic effects makes it necessary to adapt the well established computational protocols. Eventually, the methodology is tested employing various common functionals (PW91, PBE, PBE-D3, PBE0-D3, PBEsol and SCAN) by comparison to experimental and high-level results for the bulk of Cn and Og, as well as by calculating adsorption energies of Cn-Og on a gold surface and comparing these to the lighter congeners Hg-Rn as well as experimentally derived data. These tests establish that our approach provides a consistent and accurate description of the reactivity of the SHEs and is largely in excellent agreement with experimental and high-level references, and moreover underline the great relevance of dispersion interactions, as well the game-changing impact of spin-orbit coupling on SHE reactivity. Ultimately, the conducted calculations provide novel insights into the chemical behavior and nature of the SHEs, showcase the breakdown of periodic trends in the seventh period, and allow us to revisit and confirm an empirical relation between adsorption on gold and the cohesive energy.

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