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1.
Inorg Chem ; 63(24): 11494-11500, 2024 Jun 17.
Article in English | MEDLINE | ID: mdl-38838269

ABSTRACT

Aromaticity is one of the most important and widely used concepts in chemistry. Among the various experimentally discovered and theoretically predicted compounds that possess different types of aromaticity, conflicting aromaticity, where aromatic and antiaromatic electron delocalization is present in one molecule simultaneously, remains one of the most controversial and elusive concepts, although theoretically predicted 15 years ago. In this work, we synthesized a novel conflicting aromatic trirhodium complex that contains a σ-aromatic metal fragment surrounded by the π-antiaromatic organic ligand and characterized it by nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry, and X-ray single crystal structure analysis. Experimental characterization and quantum chemical calculations confirm the unique conflicting aromaticity of the synthesized trirhodium molecule. Thus, this novel conflicting aromatic molecule expands the family of aromatic compounds. This discovery will enable researchers to develop and understand the phenomena of conflicting aromaticity in chemistry.

2.
Phys Chem Chem Phys ; 25(32): 21173-21182, 2023 Aug 16.
Article in English | MEDLINE | ID: mdl-37490276

ABSTRACT

The global energy optimization problem is an acute and important problem in chemistry. It is crucial to know the geometry of the lowest energy isomer (global minimum, GM) of a given compound for the evaluation of its chemical and physical properties. This problem is especially relevant for atomic clusters. Due to the exponential growth of the number of local minima geometries with the increase of the number of atoms in the cluster, it is important to find a computationally efficient and reliable method to navigate the energy landscape and locate a true global minima structure. Newly developed neural network (NN) atomistic potentials offer a numerically efficient and relatively accurate approach for molecular structure optimization. An important question that needs to be answered is "Can NN potentials, trained on a given set, represent the potential energy surface (PES) of a neighboring domain?". In this work, we tested the applicability of ANI-1ccx and ANI-nr NN atomistic potentials for the global minima optimization of carbon clusters Cn (n = 3-10). We showed that with the introduction of the cluster connectivity restriction and consequent DFT or ab initio calculations, ANI-1ccx and ANI-nr can be considered as robust PES pre-samplers that can capture the GM structure even for large clusters such as C20.

3.
Phys Chem Chem Phys ; 25(20): 14046-14055, 2023 May 24.
Article in English | MEDLINE | ID: mdl-37161655

ABSTRACT

Microsolvated clusters of multiply charged anions play a crucial role in atmospheric chemistry and some of them were previously registered experimentally. At the same time, there are no experimental observations of [CO3·(H2O)n]2-. The reasons for this may be related to the thermodynamical or kinetical instability of microsolvated CO32- toward autoionization or autoprotonation processes. In this study we theoretically investigate the potential stability of the [CO3·(H2O)n]2- microsolvated clusters from both perspectives - thermodynamic and kinetic - and we claim they are stable toward autoionization and kinetically semi-stable toward autoprotonation. In addition, the behaviour of CO32- anions in bulk water solvent was analysed to highlight important precautions for synthetic purposes.

4.
J Comput Chem ; 44(3): 168-178, 2023 Jan 30.
Article in English | MEDLINE | ID: mdl-35385143

ABSTRACT

Recently fabricated 2D biphenylene network is an astonishing solid-state material, which possesses unique metal-like conductive properties. At the same time, two-dimensional boron nitride network (2D-BN)-an isoelectronic and structural analogue of biphenylene network, is an insulator with a wide direct bandgap. This study investigates the relationship between the electronic properties and chemical bonding patterns for these species. It is shown that the insulating 2D-BN network possesses a strong localization of electron density on the nitrogen atoms. In turn, for a carbon-containing sheet, we found a highly delocalized electron density and an appreciable overlap of pz orbitals of neighboring C6 rings, which might be a reason for the conductive properties of the material.

5.
Dalton Trans ; 52(1): 29-36, 2022 Dec 20.
Article in English | MEDLINE | ID: mdl-36421024

ABSTRACT

Carbon possesses an important ability to be in a valence state of IV, which is essential for organic chemistry and all carbon-based life forms. In turn, tin is usually observed in the valence state of II, although it is a carbon group element. This creates an open question about the possibility of the existence of tin-based "organic" molecules. In this work, we investigate hydro-tin compounds Sn2Hx (x = 1-6) and Sn3Hy (y = 1-8) via DFT and ab initio quantum chemistry methods, studying their global minimum geometry, thermodynamic stability, and chemical bonding patterns. We show that hydrogen-saturated stoichiometries (Sn2H6 and Sn3H8) are exact analogs of hydrocarbons, while unsaturated stoichiometries are characterized by multi-center bonds, aromaticity, and different valence states of tin. In addition, a refined procedure of global geometry minimization based on simulated annealing and ab initio molecular dynamics is proposed.

6.
Chem Commun (Camb) ; 58(42): 6223-6226, 2022 May 24.
Article in English | MEDLINE | ID: mdl-35510576

ABSTRACT

In this work, we synthesize naked tin cluster anion Sn368-, representing the first example of pure Sn nanowire assembled through oxidative coupling reactions of a super atomic cluster Sn94-. Theoretical analysis confirm the presence of aromaticity for each Sn9 unit showing four adjacent aromatic subunits bridged by parallel Sn-Sn bonds.

7.
Front Chem ; 10: 880804, 2022.
Article in English | MEDLINE | ID: mdl-35494656

ABSTRACT

A series of complexes of Na, K, NH4, and H3O with [bpy.bpy.bpy]cryptand, [2.2.2]cryptand, and spherical cryptand were investigated via DFT and ab initio methods. We found that by coating Rydberg molecules with the "organic skin" one could further decrease their ionization potential energy, reaching the values of ∼1.5 eV and a new low record of 1.3 eV. The neutral cryptand complexes in this sense possess a weakly bounded electron and may be considered as very strong reducing agents. Moreover, the presence of an organic cage increases the thermodynamic stability of Rydberg molecules making them stable toward the proton detachment.

8.
Nat Commun ; 13(1): 2149, 2022 Apr 20.
Article in English | MEDLINE | ID: mdl-35444180

ABSTRACT

Understanding the structural changes taking place during the assembly of single atoms leading to the formation of atomic clusters and bulk materials remains challenging. The isolation and theoretical characterization of medium-sized clusters can shed light on the processes that occur during the transition to a solid-state structure. In this work, we synthesize and isolate a continuous 24-atom cluster Ge244-, which is characterized by X-ray diffraction analysis and Energy-dispersive X-ray spectroscopy, showing an elongated structural characteristic. Theoretical analysis reveals that electron delocalization plays a vital role in the formation and stabilization of the prolate cluster. In contrast with carbon atoms, 4 s orbitals of Ge-atoms do not easily hybridize with 4p orbitals and s-type lone-pairs can be localized with high occupancy. Thus, there are not enough electrons to form a stable symmetrical fullerene-like structure such as C24 fullerene. Three aromatic units with two [Ge9] and one [Ge6] species, connected by classical 2c-2e Ge-Ge σ-bonds, are aligned together forming three independent shielding cones and eventually causing a collapse of the global symmetry of the Ge244- cluster.

9.
J Chem Inf Model ; 62(10): 2378-2386, 2022 05 23.
Article in English | MEDLINE | ID: mdl-35451847

ABSTRACT

Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the popular CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. Additional performance improvements were gained by finding more optimal process placement and affinity settings. Statistical methods were employed to understand performance changes in spite of the variability in runtime for each molecular dynamics timestep. Ideal conditions for CPU runs were found when running at least four MPI ranks per node, bound evenly across each socket. This study also showed that fully utilizing processing cores, with one OpenMP thread per core, performed better than when reserving cores for the system. The CPU-only simulations scaled at 70% or more of the ideal scaling up to 10 compute nodes, after which the returns began to diminish more quickly. Simulations on a single 40-core node with two NVIDIA V100 GPUs for acceleration achieved over 3.7× speedup compared to the fastest single 36-core node CPU-only version. These same GPU runs showed a 13% speedup over the fastest time achieved across five CPU-only nodes.


Subject(s)
Molecular Dynamics Simulation , Software
10.
Molecules ; 26(23)2021 Nov 29.
Article in English | MEDLINE | ID: mdl-34885812

ABSTRACT

A chemical bonding of several metallabenzenes and metallabenzynes was studied via an adaptive natural density partitioning (AdNDP) algorithm and the induced magnetic field analysis. A unique chemical bonding pattern was discovered where the M=C (M: Os, Re) double bond coexists with the delocalized 6c-2e π-bonding elements responsible for aromatic properties of the investigated complexes. In opposition to the previous description where 8 delocalized π-electrons were reported in metallabenzenes and metallabenzynes, we showed that only six delocalized π-electrons are present in those molecules. Thus, there is no deviation from Hückel's aromaticity rule for metallabenzynes/metallabenzenes complexes. Based on the discovered bonding pattern, we propose two thermodynamically stable novel molecules that possess not only π-delocalization but also retain six σ-delocalized electrons, rendering them as doubly aromatic species. As a result, our investigation gives a new direction for the search for carbon-metal doubly aromatic molecules.

11.
J Phys Chem A ; 125(40): 8899-8906, 2021 Oct 14.
Article in English | MEDLINE | ID: mdl-34591472

ABSTRACT

Investigation of the process of the NO3- anion solvation is central to understanding the chemical and physical properties of its aqueous solutions. The importance of this topic can be seen in atmospheric chemistry, as well as in nuclear waste processing research. In this work, we used a particle swarm optimization technique driven by density functional theory to sample the potential energy surface of various microsolvated [NO3·(H2O)n]- (n = 1-12) clusters. We found that the charge transfer plays a crucial role in the stabilization of the investigated species. Moreover, by conducting ab initio molecular dynamics simulations, we showed that at low concentrations (∼0.2 M) the NO3- species tend to be located on the surface of water solution. We also observed that the contact ion pair K+-NO3- undergoes a fast dissociation and each of the ions is solvated separately. As a result, from our calculations, we expect that at low concentration there could be oppositely signed concentration gradients for NO3- and K+ ions in a thin water film.

13.
Nat Commun ; 12(1): 4465, 2021 Jul 22.
Article in English | MEDLINE | ID: mdl-34294702

ABSTRACT

Heterometallic clusters have attracted broad interests in the synthetic chemistry due to their various coordination modes and potential applications in heterogeneous catalysis. Here we report the synthesis, experimental, and theoretical characterizations of four ternary clusters ([M2(CO)6Sn2Sb5]3- (M = Cr, Mo), and [(MSn2Sb5)2]4-, (M = Cu, Ag)) in the process of capturing the hypho- [Sn2Sb5]3- in ethylenediamine (en) solution. We show that the coordination of the binary anion to transition-metal ions or fragments provides additional stabilization due to the formation of locally σ-aromatic units, producing a spherical aromatic shielding region in the cages. While in the case of [Mo2(CO)6Sn2Sb5]3- stabilization arises from locally σ-aromatic three-centre and five-centre two-electron bonds, aromatic islands in [(AgSn2Sb5)2]4- and [(CuSn2Sb5)2]4- render them globally antiaromatic. This work describes the coordination chemistry of the versatile building block [Sn2Sb5]3-, thus providing conceptual advances in the field of metal-metal bonding in clusters.

14.
J Phys Chem A ; 125(26): 5726-5737, 2021 Jul 08.
Article in English | MEDLINE | ID: mdl-34184903

ABSTRACT

The mechanism of ketones homogeneous hydrogenation with t-BuOK in tert-butanol is currently portrayed as the one proceeding via a six-membered [2 + 2 + 2] cyclic transition state involving the H2 molecule, the base, and a ketone. However, the concerted nature of the reaction is inconsistent with a number of experimental observations. Here we reanalyze available experimental data and revise the mechanism of this paradigmatic reaction based on the static and dynamic density functional theory (DFT) calculations in solution phase. In contrast to the gas-phase profile where the overall reaction occurs in two elementary steps, there are three consecutive steps in solution: cleavage of the H-H bond in basic tert-butanol to afford potassium hydride, addition of potassium hydride across the C═O bond of a ketone through the rate-determining transition state, and rapid product formation through K/H exchange. Potassium hydride is therefore an important intermediate of the catalytic process. The free energy profile for the prophetic ester homogeneous hydrogenation with t-BuOK in tert-butanol is also computed herein. The reaction seems to be kinetically possible, but slightly harsher conditions need to be applied, consistent with rate-determining nature of the potassium hydride addition.

15.
Angew Chem Int Ed Engl ; 60(18): 9990-9995, 2021 Apr 26.
Article in English | MEDLINE | ID: mdl-33682237

ABSTRACT

Since [Sn8 ]6- was discovered from the solid-state phase in 2000, its solution chemistry has been elusive due to the high charges and chemical activity. Herein, we report the synthesis and characterization of an inverse sandwich-type cluster dimer {[K2 ZnSn8 (ZnMes)]2 }4- (1 a), in which the highly charged [Sn8 ]6- is captured by mixed-valence ZnI /ZnII to form the dimer {closo-[Zn2 Sn8 ]}2 moieties bridged by a Zn-Zn bond. Such Zn-Sn cluster not only exhibits a novel example of mixed-valence ZnI /ZnII for stabilizing highly active anion species, but also indicates the [Sn8 ]6- cluster can act as a novel bridging ligand, like arene, with a η4 :η4 -fashion. Theoretical calculations indicate that a significant delocalization of electrons over Zn atoms plays a vital role in the stabilization of the [Sn8 ]6- species. The AdNDP and magnetic response analyses clearly showed the presence of local σ-aromaticity in three cluster fragments: two ZnSn4 caps and Sn8 square antiprism.

16.
J Phys Chem Lett ; 12(1): 32-40, 2021 Jan 14.
Article in English | MEDLINE | ID: mdl-33296213

ABSTRACT

We conducted a joint experimental-theoretical investigation of the high-pressure chemistry of europium polyhydrides at pressures of 86-130 GPa. We discovered several novel magnetic Eu superhydrides stabilized by anharmonic effects: cubic EuH9, hexagonal EuH9, and an unexpected cubic (Pm3n) clathrate phase, Eu8H46. Monte Carlo simulations indicate that cubic EuH9 has antiferromagnetic ordering with TN of up to 24 K, whereas hexagonal EuH9 and Pm3n-Eu8H46 possess ferromagnetic ordering with TC = 137 and 336 K, respectively. The electron-phonon interaction is weak in all studied europium hydrides, and their magnetic ordering excludes s-wave superconductivity, except, perhaps, for distorted pseudohexagonal EuH9. The equations of state predicted within the DFT+U approach (U - J were found within linear response theory) are in close agreement with the experimental data. This work shows the great influence of the atomic radius on symmetry-breaking distortions of the crystal structures of superhydrides and on their thermodynamic stability.

17.
Nat Commun ; 11(1): 5286, 2020 10 20.
Article in English | MEDLINE | ID: mdl-33082326

ABSTRACT

Sandwich-type clusters with the planar fragment containing a heterometallic sheet have remained elusive. In this work, we introduce the [K(2,2,2-crypt)]4{(Ge9)2[η6-Ge(PdPPh3)3]} complex that contains a heterometallic sandwich fragment. The title compound is structurally characterized by means of single-crystal X-ray diffraction, which reveals the presence of an unusual heteroatomic metal planar fragment Ge@Pd3. The planar fragment contains a rare formal zerovalent germanium core and a peculiar bonding mode of sp2-Ge@(PdPPh3)3 trigonal planar structure, whereas the nonagermanide fragments act as capping ligands. The chemical bonding pattern of the planar fragment consists of three 2c-2e Pd-Ge σ-bonds attaching Pd atoms to the core Ge atom, while the binding between the planar fragment and the aromatic Ge9 ligands is provided by six 2c-2e Pd-Ge σ-bonds and two delocalized 4c-2e σ-bonds. The synthesized cluster represents a rare example of a sandwich compound with the heteroatomic metal planar fragment and inorganic aromatic capping ligands.

18.
Inorg Chem ; 59(15): 10404-10408, 2020 Aug 03.
Article in English | MEDLINE | ID: mdl-32674579

ABSTRACT

This research reports a search for peculiar monobridged structures of the E2H2 molecules (E = Be, Mg, Ca, Sr, Ba). For Be2H2 and Mg2H2, the monobridged geometry is not an equilibrium but rather a transition state between the vinylidene-like structure and the global minimum HE-EH linear geometry. However, for Ca2H2, Sr2H2, and Ba2H2, this situation changes significantly; the linear structure is no longer the global minimum but lies higher in energy than two other equilibria, the dibridged and monobridged structures. The planar dibridged structures of both Sr2H2 and Ba2H2 should be observable via IR spectroscopy. Although the remarkable monobridged structures lie 8.3 (Sr) and 7.6 kcal/mol (Ba) higher, the large IR intensities of the terminal E-H stretching frequencies may make the monobridged structures observable. The monobridged structures have sizable permanent dipole moments (3.07 and 3.06 D for Sr and Ba, respectively) and also should be observable via microwave spectroscopy.

19.
Angew Chem Int Ed Engl ; 59(39): 17286-17290, 2020 Sep 21.
Article in English | MEDLINE | ID: mdl-32608037

ABSTRACT

In this work, the largest heterometallic supertetrahedral clusters, [Zn6 Ge16 ]4- and [Cd6 Ge16 ]4- , were directly self-assembled through highly-charged [Ge4 ]4- units and transition metal cations, in which 3-center-2-electron σ bonding in Ge2 Zn or Ge2 Cd triangles plays a vital role in the stabilization of the whole structure. The cluster structures have an open framework with a large central cavity of diameter 4.6 Šfor Zn and 5.0 Šfor Cd, respectively. Time-dependent HRESI-MS spectra show that the larger clusters grow from smaller components with a single [Ge4 ]4- and ZnMes2 units. Calculations performed at the DFT level indicate a very large HOMO-LUMO energy gap in [M6 Ge16 ]4- (2.22 eV), suggesting high kinetic stability that may offer opportunities in materials science. These observations offer a new strategy for the assembly of heterometallic clusters with high symmetry.

20.
Chem Commun (Camb) ; 56(48): 6583-6586, 2020 Jun 16.
Article in English | MEDLINE | ID: mdl-32400811

ABSTRACT

In this work, we report a dimeric cluster anion, {[CuGe9Mes]2}4-, which was isolated as the [K(2,2,2-crypt)]+ salt and characterized by using single-crystal X-ray diffraction and ESI mass spectroscopy. The title cluster represents the first locally σ-antiaromatic compound in the solid state, as well as the first heteroatomic antiaromatic compound.

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