Neural network atomistic potentials for global energy minima search in carbon clusters

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.

On the existence of CO32- microsolvated clusters: a theoretical study

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 CO₃^2- 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 CO₃^2- anions in bulk water solvent was analysed to highlight important precautions for synthetic purposes.

Overlapping electron density and the global delocalization of π-aromatic fragments as the reason of conductivity of the biphenylene network

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 p_z orbitals of neighboring C₆ rings, which might be a reason for the conductive properties of the material.

Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs

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.

Symmetry collapse due to the presence of multiple local aromaticity in Ge244

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.

Gaining insight on the structural transformations from atomic clusters to bulk materials is challenging. Here the authors synthesize a continuous cluster of germanium Ge₂₄⁴⁻, which can be viewed as two terminal Ge₉ units bridged via a Ge₆ central fragment, and characterize it by several techniques including X-ray diffraction; theoretical analysis indicates the presence of three aligned independent aromatic fragments.

Superalkali Coated Rydberg Molecules

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.

Sn368‒: A 2.7 nm Naked Aromatic Tin Rod

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...

Occurrence of Double Bond in π-Aromatic Rings: An Easy Way to Design Doubly Aromatic Carbon-Metal Structures

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.

DFT Study of Microsolvated [NO3·(H2O)n]- (n = 1-12) Clusters and Molecular Dynamics Simulation of Nitrate Solution

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.

Ternary aromatic and anti-aromatic clusters derived from the hypho species [Sn2Sb5]3

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.

Mechanism of Potassium tert-Butoxide-Catalyzed Ketones Hydrogenation in the Solution Phase

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.

[Sn8 ]6- -Bridged Mixed-Valence ZnI /ZnII in {[K2 ZnSn8 (ZnMes)]2 }4- Inverse Sandwich-Type Cluster Supported by a ZnI -ZnI Bond

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 Zn^I /Zn^II 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 Zn^I /Zn^II 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.

Novel Strongly Correlated Europium Superhydrides

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 T_N of up to 24 K, whereas hexagonal EuH₉ and Pm3n-Eu₈H₄₆ possess ferromagnetic ordering with T_C = 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.

Hydrogen peroxide assisted photorelease of an anthraquinone-based ligand from [Ru(2,2'-bipyridine)2(9,10-dioxo-9,10-dihydroanthracen-1-olate)]Cl in aqueous solution

A new class of light-activated ruthenium(ii) complex was designed as a potential blocker of biological functioning, especially for targeting redox reactions within mitochondria under light activation. Based on our concepts the complex [Ru(bipy)2(1-hydroxyanthra-9,10 quinone)]Cl (RU1) was prepared and studied to understand the preliminary reaction mechanisms and its excited state behaviour through a series of stability tests, electrochemistry, UV-Visible kinetics and femtosecond transient absorption spectroscopy experiments. Under white light in the presence of H2O2 two different reactions (fast and slow) appear to take place. The complex loses the quinone-based ligand and a resulting Ru(iii) or Ru(v) species is produced. The complex RU1 shows potential to consume H2O2 from the one carbon metabolism in mitochondria, and hence may cut the energy cycle pathway of tumor cells.

Dibridged, Monobridged, Vinylidene-Like, and Linear Structures for the Alkaline Earth Dihydrides Be2H2, Mg2H2, Ca2H2, Sr2H2, and Ba2H2. Proposals for Observations

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.

Stability, electronic, and optical properties of two-dimensional phosphoborane

The structure and properties of two-dimensional phosphoborane sheets were computationally investigated using Density Functional Theory calculations. The calculated phonon spectrum and band structure point to dynamic stability and allowed characterization of the predicted two-dimensional material as a direct-gap semiconductor with a band gap of ~1.5 eV. The calculation of the optical properties showed that the two-dimensional material has a relatively small absorptivity coefficient. The parameters of the mechanical properties characterize the two-dimensional phosphoborane as a relatively soft material, similar to the monolayer of MoS₂ . Assessment of thermal stability by the method of molecular dynamics indicates sufficient stability of the predicted material, which makes it possible to observe it experimentally.

All-metal σ-antiaromaticity in dimeric cluster anion {[CuGe9Mes]2}4

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.

Record Low Ionization Potentials of Alkali Metal Complexes with Crown Ethers and Cryptands

Electronic properties of series of alkali metals complexes with crown ethers and cryptands were studied via DFT hybrid functionals. For [M([2.2.2]crypt)] (M=Li, Na, K) extremely low (1.70-1.52 eV) adiabatic ionization potentials were found. Such low values of ionization energies are significantly lower than those of alkali metal atoms. Thus, the investigated complexes can be defined as superalkalis. As a result, our investigation opens up new directions in the designing of chemical species with record low ionization potentials and extends the explanation of the ability of the cryptates and alkali crown ether complexes to stabilize multiple charged Zintl ions.

Multiple local σ-aromaticity of nonagermanide clusters

A new chemical bonding picture of various nonagermanide species were presented. The stability of Ge₉ fragments could be well described via the concept of multiple local σ-aromaticity.

Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge₉]^4–, [Ge₉{P(NH₂)₂}₃]^–, Cu[Ge₉{P(NH₂)₂}₃] and Cu(NHC)[Ge₉{P(NH₂)₂}₃]) and obtained a simple and chemically intuitive bonding pattern which can explain the variety of active sites and the existence of both D_3h and C_4v geometries for such clusters. Moreover, the [Ge₉]^4– core is found to be a unique example of an inorganic Zintl cluster with multiple local σ-aromaticity.

Superoctahedral two-dimensional metallic boron with peculiar magnetic properties

A novel two-dimensional ferromagnetic stable boron material has been predicted and exhaustively studied with DFT methods. Its magnetism can be described by the presence of two unpaired delocalized bonding elements inside each distorted octahedron.

Chemical bonding analysis of excited states using the adaptive natural density partitioning method

A novel approach to chemical bond analysis for excited states has been developed. Using an extended adaptive natural density partitioning method (AdNDP) as implemented in AdNDP 2.0 code, we obtained chemically intuitive bonding patterns for the excited states of H2O, B5+, and C2H4+ molecules. The deformation pathway in the excited states could be easily predicted based on the analysis of the chemical bond pattern. We expect that this new method of chemical bonding analysis would be very helpful for photochemistry, photoelectron spectroscopy, electron spectroscopy and other chemical applications that involved excited states.

Photoinduced hole transfer in QD-phthalocyanine hybrids

A series of CdSe quantum dot (QD)-phthalocyanine (Pc) hybrids were synthesized and their photophysics was studied using steady state and time-resolved spectroscopic methods. Emission of QDs was progressively quenched upon increasing the concentration of Pc in the hybrids. A detailed transient absorption study of the hybrids revealed that the mechanism of quenching is charge separation, resulting in the formation of hybrids with negatively charged QDs and the Pc cation. Direct photo-excitation of Pc did not show any detectable interaction between the excited state of Pc and the QD to which it is attached. An explanation is proposed, based on the suggestion that the energy of the lowest unoccupied molecular orbital (LUMO) of Pc is lower than the lower edge of the QD conduction band, while the energy of the highest occupied molecular orbital (HOMO) of Pc is sufficiently higher than the high energy edge of the QD valence band (VB), thus permitting hole transfer from the QD VB to the Pc HOMO after photo-excitation of QDs.

[Optimization of directed training loads on the respiratory system]

Potentiality of an increased elastic resistance to respiratory movements in improving the functional conditioning of young athletes was evaluated. Training with increased elastic resistance to respiration brought about gains in strength and endurance of the respiratory muscles, growth of the maximal oxygen consumption, work ability, and special physical fitness of athletes.

Kinetics of photo-active bacteriorhodopsin analog 3,4-didehydroretinal

Kinetics of the photo-induced processes of the transient states of the 3,4-didehydroretinal (3,4-dhr) modified bacteriorhodopsin (bR) was studied by a flash photolysis method in a water suspension at room temperature. The excitation initiated a photocycle with several transient intermediates similar to the trans photocycle of native bR. The main observation of the study was that although major part (80%) of the population of the M state relaxed via the O intermediate as in natural bR, 20% relaxed directly to the bR ground state in 200 ms.

Charge-transfer emission of compact porphyrin-fullerene dyad analyzed by Marcus theory of electron-transfer

A porphyrin-fullerene dyad, which is characterized by a close proximity of the porphyrin donor and the fullerene acceptor, was found to undergo a photoinduced electron transfer both in solutions and in solid films. Near-infrared charge-transfer (CT) emission was observed and analyzed in frame of the semi-classical Marcus electron-transfer theory yielding values for the reaction free energy, -deltaG degrees = 1.75 eV, the internal reorganization energy, lambdav = 0.05 eV, and the donor-acceptor vibrational energy, hv(v) = 0.14 eV, both in solution and in solid film. The influence of the environment on the CT properties of the dyad is described by a single parameter, the outer-sphere reorganization energy, lambdas, which varies from 0.05 eV in non-polar solvents and films to 0.13 eV in solvents of moderate polarity. At low temperatures (T< 200 K), the CT emission consists of distinct bands shifted from each other by value hv(v). This is the first direct observation of the vibrational frequencies of a porphyrin-fullerene donor-acceptor system.

[Folic acid in the combined treatment of patients with disseminated sclerosis and chronic gastritis]

Folic acid was used for the complex treatment of patients with multiple sclerosis. The doses employed were 200-300 mcg daily. It was established that folic acid improved the reparative processes in the gastric mucosa and produced a pronounced therapeutic effect on the neurological status of the patients, favoured improvement of their general condition.