Global Minimum Energy Structure Research Articles

APPLYING THE GENETIC ALGORITHM AND QUANTUM CHEMICAL CALCULATIONS TO STUDY THE STRUCTURE OF THE Sc2B6 CLUSTER AND ITS CO ADSORPTION

We used the genetic algorithm and quantum chemical calculations to study the structures of the Sc2B6 cluster. The global minimum energy structure has the shape of a hexagonal bipyramid with an Sc atom at each apex and a B6 ring that belongs to the D6h point group symmetry. The second most stable structure has the Cs point group symmetry and can be formed by substituting a Sc atom for a B atom in the ring and a B atom for Sc in one of the apexes. From the computational results, the Sc2B6 cluster is found to be a good candidate to form a nanomaterial for treating CO gas.

Sr2B8: A new member to the [formula omitted] and π double aromaticity

In this paper, we have employed the CALYPSO method to perform structure search on the Sr2Bn0/− (n = 1–12) clusters, resulting in the determination of the global energy minimum structures. Moreover, we have conducted PES simulations on each of the obtained structures with the aim of comparing them to experimental data. Upon comparison, we have identified a relatively more stable inverse sandwich structure Sr2B8, and have conducted an analysis of its internal atomic bonding characteristics. The results indicate that there is a significant transfer of valence electrons from the Sr atoms to the B atoms, leading to the occupied orbitals being predominantly contributed by the valence shell of the B atoms. The B atoms are interconnected by covalent single bonds to form a ring structure, with the two Sr atoms positioned on either side of the B ring, binding to the ring through ionic bonds. The entire Sr2B8 exhibits double aromaticity by the delocalized σ occupied orbitals and the delocalized π occupied orbitals.

The unique geometries and magnetic anisotropy energy of FenPt (n = 3–13) clusters: A first-principles investigation

Enthusiasm for exploring magnetic anisotropy energy (MAE) and spin–orbit coupling (SOC) effects in magnetic studies of transition metal alloy clusters remains high. In this paper, the first-principle method was used to investigate the global minimum energy structure of FenPt (n = 3–13) clusters and their interesting magnetic properties. Comparative structural analyses show that FenPt (n = 3–13) clusters have unique structures, and their relative stability analyses indicate that the increase in the number of atoms influences the geometrical arrangement of the clusters. The exploration of magnetic properties has focused on two areas. First, FenPt (n = 3–13) is found to have a large magnetic moment, while the magnetic moment increment surprisingly varies in the same way in different cases with and without the inclusion of SOC effects. Second, the calculations show that FenPt (n = 3, 4, 9, 13) has MAE, ranging from 1.420-2.687 meV/atom. The SOC matrix results show the interaction of Pt dx2-y2 and Pt dxy, and the interaction of Pt dz2 and Pt dyz, exhibit an indispensable force in determining the MAE.

Chemical Correlation of Cistendiol Obtained from Cativic Acid in Two Different Pathways

Objective This study aims to convert cativic acid, which was isolated from Ageratina jocotepecana, into cistendiol (5), an analog of cistenolic acid isolated from Cistus symphytifolius. The position of hydroxyl at C-7 in compound 5 could be achieved by applying the Schenck reaction with singlet oxygen (1O2) through photooxidation reaction of 6. Additionally, epoxidation reaction of 1, followed by further reduction and acid treatment, can serve as another pathway to obtain compound 5. Methods Cativic acid was isolated from Ageratina jocotepecana flowers, reduction methodology was realized with THF and LiAlH4, epoxidation reaction was carried out with mCPBA in CH2Cl2 and K2CO3, oxidation of alcohol with PCC in CH2Cl2 and MgSO4, photooxidation reaction was realized with blue and white light using singlet oxygen (1O2) and photosensitizers such as eosin, methylene blue and Ru(bpy)3(PF6)2 in acetonitrile. Geometry optimizations for transition states were performed using MMFF94 with Monte Carlo protocol, and GDFT was used B3LYP/DGDZVP level of theory with Gaussian 09. Results Cistendiol was synthesized by photooxidation reaction of 6 with Ru(bpy)3(PF6)2 and air such oxidant with a ratio of 8:1, while epoxidation of 1 further reduction and acid treatment afforded cistendiol with a ratio of 9:1, the ratio was determined by NMR, additionally the global minimum energy structures GDFT calculated values supports the results described by NMR ratio. The stereochemistry was also confirmed by NOESY experiment and the comparison is in agreement with literature data. Conclusion Herein, we described the conversion of cativic acid isolated from Ageratina jocotepecana employing a new photooxidation methodology and classic epoxidation techniques, to produce an analog of cistenolic acid isolated from Cistus symphytifolius. The results, which include Supplemental material, enable comparison of stereochemistry, specifically the 13 S for C-13 of Ageratina jocotepecana with other compounds such as cistenolic or salvic acid, which had been the subject of study by researchers.

Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters.

The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular clusters. However, QC calculations heavily depend on the chosen computational method, and when dealing with large systems, striking a balance between accuracy and computational cost becomes essential. We benchmarked the binding energies and structures and found the B97-3c method to be a good compromise between the accuracy and computational cost for studying large cluster systems. Further, we carefully assessed configurational sampling procedures for targeting large atmospheric molecular clusters containing up to 30 molecules (approximately 2 nm in diameter) and proposed a funneling approach with highly improved accuracy. We find that several parallel ABCluster explorations lead to better guesses for the cluster global energy minimum structures than one long exploration. This methodology allows us to bridge computational studies of molecular clusters, which typically reach only around 1 nm, with experimental studies that often measure particles larger than 2 nm. By employing this workflow, we searched for low-energy configurations of large sulfuric acid-ammonia and sulfuric acid-dimethylamine clusters. We find that the binding free energies of clusters containing dimethylamine are unequivocally more stable than those of the ammonia-containing clusters. Our improved configurational sampling protocol can in the future be applied to study the growth and dynamics of large clusters of arbitrary compositions.

Influence of heteroatoms and substituents on structural and spectroscopic parameters of saturated six-member ring heterocycles: experimental and theoretical study of 1-methyl-1-germacyclohexane

The conformational analysis of newly synthesized compound, 1-methyl-1-germacyclohexane, is performed by means of a combined vibrational spectroscopy and theoretical methods. The liquid 1-methyl-1-germacyclohexane at room temperature is investigated using conventional ATR-FTIR, FT-IR (gas phase) and Raman methods. FT-IR spectra of the isolated in low-temperature neon and nitrogen matrices are registered. The further detailed vibrational conformational analysis is performed utilizing density functional theory and perturbation theory based methods. All possible 12 canonical ring conformations considering axial/equatorial CH3 group position are analyzed by utilizing DFT/B3LYP, DFT/M06-2X and MP2 at aug-cc-pVTZ theory level.The most stable conformer with the global energy minimum structure in the chair axial conformation is investigated in detail. Analysis of the potential energy surface reveals transition states (TS) and energy barriers. The conformational path is found to be as follows: chair (1C4)→ envelope/half-chair (TS)→ skew-boat (1S3 - C1 symmetry)→ boat (TS)→ skew-boat (1S5 - C2 symmetry). The energy barrier for 1C4 (chair) to 1S3 (skew-boat) conversion is 4.8 kcal/mol while for the reverse process equals to 0.5 kcal/mol.A similar conformational analysis is performed for different configurations of germacyclohexane, silacyclohexane and cyclohexane with mono- and disubstituents: CH2Cl, CH3, Cl and F. Such approach enables investigation of influence of the heteroatoms and substituents of various size and type on the structural parameters and conformational diversity.

Molecular structure, electronic, topology and non-covalent interaction of 4-(Bis(2-chloroethyl)amino)-L-phenylalanine- Anti-blood cancer activity

In this study, it is attempted to scrutinize the global minimum energy structure of anti-blood cancer drug 4-(Bis(2-chloroethyl)amino)-L-phenylalanine (4B2CA-LPA) and functionalized density functional theory (DFT) calculations regarding their geometries, topological features of covalent, non-covalent interactions with employing Atoms in molecule (AIM) and Reduced density gradient (RDG) studies. As per the topological results, a new type of non-covalent attraction forces of hydrogen-hydrogen interaction was found in this molecule. Electrostatic potential variation as well as global reactive descriptor energy variations in the solvation phases was carried out by molecular electrostatic potential (MEP) and frontier molecular orbitals (FMOs) analysis. Moreover, the electronic excitations in liquids of 4B2CA-LPA were evaluated in UV-Vis absorptions. The local bonding electron transitions and optical properties of the compound were examined with natural bond orbital (NBO) studies. The 4B2CA-LPA molecule can serve as lead molecules for the growth of anti-blood cancer drugs. Molecular docking investigation has also been carried out to determine the ability of target molecules to bind with Hematopoietic inhibitors in blood cells.

Magic Numbers and Stabilities of Photoionized Water Clusters: Computational and Experimental Characterization of the Nanosolvated Hydronium Ion.

The stability and distributions of small water clusters generated in a supersonic beam expansion are interrogated by tunable vacuum ultraviolet (VUV) radiation generated at a synchrotron. Time-of-flight mass spectrometry reveals enhanced population of various protonated water clusters (H+(H2O)n) based upon ionization energy and photoionization distance from source, suggesting there are "magic" numbers below the traditional n = 21 that predominates in the literature. These intensity distributions suggest that VUV threshold photoionization (11.0-11.5 eV) of neutral water clusters close to the nozzle exit leads to a different nonequilibrium state compared to a skimmed molecular beam. This results in the appearance of a new magic number at 14. Metadynamics conformer searches coupled with modern density functional calculations are used to identify the global minimum energy structures of protonated water clusters between n = 2 and 21, as well as the manifold of low-lying metastable minima. New lowest energy structures are reported for the cases of n = 5, 6, 11, 12, 16, and 18, and special stability is identified by several measures. These theoretical results are in agreement with the experiments performed in this work in that n = 14 is shown to exhibit additional stability, based on the computed second-order stabilization energy relative to most cluster sizes, though not to the extent of the well-known n = 21 cluster. Other cluster sizes that show some additional energetic stability are n = 7, 9, 12, 17, and 19. To gain insight into the balance between ion-water and water-water interactions as a function of the cluster size, an analysis of the effective two-body interactions (which sum exactly to the total interaction energy) was performed. This analysis reveals a crossover as a function of cluster size between a water-hydronium-dominated regime for small clusters and a water-water-dominated regime for larger clusters around n = 17.

Generating candidates in global optimization algorithms using complementary energy landscapes.

Global optimization of atomistic structure relies on the generation of new candidate structures in order to drive the exploration of the potential energy surface (PES) in search of the global minimum energy structure. In this work, we discuss a type of structure generation, which locally optimizes structures in complementary energy (CE) landscapes. These landscapes are formulated temporarily during the searches as machine learned potentials (MLPs) using local atomistic environments sampled from collected data. The CE landscapes are deliberately incomplete MLPs that rather than mimicking every aspect of the true PES are sought to become much smoother, having only a few local minima. This means that local optimization in the CE landscapes may facilitate the identification of new funnels in the true PES. We discuss how to construct the CE landscapes and we test their influence on the global optimization of a reduced rutile SnO2(110)-(4 × 1) surface and an olivine (Mg2SiO4)4 cluster for which we report a new global minimum energy structure.

Global Optimization: A Soft Computing Perspective

Tackling the problem of global optimization is one of the most important domains that physicists and chemists are working on. The use of soft computing (SC) techniques has made this easier by reducing nonlinearity and instability and making it technologically rich. This Perspective aims at explaining the basic mathematical models of the most efficient and commonly used SC techniques in computational chemistry for finding the global minimum (GM) energy structures of chemical systems. In this Perspective, we discuss the global optimizations of several chemical systems that our group has worked on using CNN, PSO, FA, ABC, BO, and some hybrid techniques, two of which are interfaced to achieve better-quality results.

Structural evolution, electronic and magnetic properties investigation of V3Sin− (n = 14–18) clusters based on photoelectron spectroscopy and density functional theory calculations

Silicon clusters doped with a transition metal (TM) atom have been intensively studied due to their novel properties and superior stability for possible usage as building blocks of future nanoelectronics. Besides the selection of the doped element, introducing the number of dopant atoms as another dimension adds versatility to tuning the cluster properties. However, there are few studies of silicon clusters doped with multiple TM atoms. Here, we present a study of V3Sin− (n = 14–18) by combining high-resolution photoelectron spectroscopy (PES) measurements with a search of their global minimum energy structures based on a homemade genetic algorithm coupled with density functional theory (DFT) for energy calculations. The simulated photoelectron spectra of the putative global minimum structures are in fair agreement with the experimental ones, which gives evidence for their authenticity as the ground-state structures. In these clusters the three V atoms always bond with each other and form an acute triangle, which can be seen as a nanoscale analogue of phase segregation in the bulk. For the size range n = 14–17, each of the ground-state structures has a silicon basket-like structure with the vanadium triangle inside, while V3Si18− has a baseball-mitt-like structure almost completely encapsulating the V3 triangle. The average binding energy of TMSin− (TM = V1, V2, V3) indicates that the more V atoms are doped the more stable the clusters are. Among these clusters, only V3Si14− have a total magnetic moment of 2 μB, making it a potential structural unit for magnetic storage devices. Mulliken population analysis and the electron spin density show that V atoms at different positions have different contributions to the total magnetic moments, and d electrons in V atoms contribute the most.

Electronic structure and reactivity indexes of cobalt clusters, both pure and mixed with NO and [Formula: see text] ([Formula: see text], [Formula: see text] and [Formula: see text]).

Among the most popular motivations for environmental scientists is improving materials that could be useful to fight or avoid pollution. This work shows a study of neutral and cationic cobalt clusters from 4 to 9 atoms ([Formula: see text], q = 0,1 and n = 4-9) to model their separate interaction with contaminant nitric and nitrous oxides. This study is within the framework of the density functional theory in the Kohn-Sham scheme by using BPW91 functional and 6-311G and 6-31G* basis sets to calculate global and local reactivity indexes. The effect of spin multiplicity is also determined. Results on the geometries of pure cobalt clusters agree with previously reported structures. Global minimum energy structures showed a marked preference towards the interaction of nitric and nitrous oxide molecules with cobalt clusters through chemisorptive dissociation, with the dissociation of the corresponding nitrogen oxide. Reactivity indexes reveal an even-odd alternate, which is related to electron counts. Moreover, the chemical potential is lowering after interaction with nitrogen oxides. The Fukui function illustrates the reactive zones with a high probability of chemisorption of more nitrogen oxide molecules.

Dimerization dynamics of carboxylic acids in helium nanodroplets.

The dimerization of molecules in helium nanodroplets is known to preferentially yield structures of higher energy than the global energy minimum structure for a number of quite different monomers. Here, we explore dimerization in this environment using an atomistic model within statistically converged molecular dynamics (MD) trajectories, treating the solvent implicitly through the use of a thermostat, or more explicitly by embedding one monomer in a He100 cluster. The focus is on the two simplest carboxylic acids, formic and acetic, both of which have been studied experimentally. While the global minimum structure, which comprises two CO⋯HO hydrogen bonds, is predicted to be the most abundant dimer in the absence of the helium solvent, this is no longer the case once helium atoms are included. The simulations confirm the importance of kinetic trapping effects and also shed light on the occurrence of specific dynamical effects, leading to the occasional formation of high-energy structures away from minima, such as saddle configurations. Theoretically predicted infrared spectra, based on the MD statistics, are in good agreement with the experimental spectra.

Exploring the potential energy surface of nCO2 (n = 1–5) capture by imidazole-and fluorine-based ionic liquids: A DFT study

One of the reasons for global warming is the rising of greenhouse gasses causing the planet's temperature to increase; among these gases, CO2 accounts for 80%. For this reason, it is essential to contemplate environmentally sustainable alternatives for CO2 capture and storage, such as the use of ionic liquids (ILs), which represent an excellent option due to their high affinity for CO2. This theoretical study considered ILs based on imidazole ([bmim]+ and [emim]+) and fluorinated ([TFSI]- and [PF6]-) dimers, thorough exploration of the potential energy surfaces of nCO2[bmim]+[PF6]−, nCO2[emim]+[TFSI]−, nCO2[bmim]+[PF6]− and nCO2[emim]+[TFSI]− molecular clusters, n = 1–5, by using a stochastic SnippetKick searching algorithm. Followed by the optimisation of the molecular cluster geometries using Density Functional Theory (DFT) calculations to describe the effect of physisorption of up to five CO2 in ILs. It was revealed an aggregation of CO2 molecules between the imidazole ring and the anion, mainly surrounding [TFSI]- or [PF6]-, in the form of an orbital in putative global minimum-energy structures, which allows a higher CO2 physisorption. Finally, a detailed analysis of the thermodynamic properties and intermolecular interactions between ILs and CO2 molecules was performed with different approximations of the electron density scalars. Overall, this confirms the use of the ILs studied to capture CO2 efficiently.

Machine learning potential aided structure search for low-lying candidates of Au clusters

A machine learning (ML) potential for Au clusters is developed through training on a dataset including several different sized clusters. This ML potential accurately covers the whole configuration space of Au clusters in a broad size range, thus expressing a good performance in search of their global minimum energy structures. Based on our potential, the low-lying structures of 17 different sized Au clusters are identified, which shows that small sized Au clusters tend to form planar structures while large ones are more likely to be stereo, revealing the critical size for the two-dimensional (2D) to three-dimensional (3D) structural transition. Our calculations demonstrate that ML is indeed powerful in describing the interaction of Au atoms and provides a new paradigm on accelerating the search of structures.

CSinGe4-n2+ (n = 1-3): prospective systems containing planar tetracoordinate carbon (ptC).

Density functional theory (DFT) based calculations have been carried out to explore the potential energy surface (PES) of CSinGe4-n2+/+/0 (n = 1-3) systems. The global minimum structures in the di-cationic states (1a, 1b, and 1c) contain a planar tetracoordinate carbon (ptC). For the CSi2Ge22+ system, the second stable isomer (2b) also contains a ptC with 0.67 kcal mol-1 higher energy than that of the 1b ptC isomer. The global minima of the neutral and mono-cationic states of the designed systems are not planar. The 1a, 1b, and 1c structures follow the 18 valence electron rule. The relative energies of the low-lying isomers of CSiGe32+, CSi2Ge22+, and CSi3Ge2+ systems with respect to the global minima were calculated using the CCSD(T)/aug-cc-pVTZ method. Ab initio molecular dynamics simulations for 50 ps time indicate that all the global minimum structures (1a, 1b, and 1c) are kinetically stable at 300 K and 500 K temperatures. The natural bond orbital (NBO) analysis suggests strong σ-acceptance of the ptC from the four surrounding atoms and simultaneously π-donation occurs from the ptC center. The nucleus independent chemical shift (NICS) showed σ/π-dual aromaticity. We hope that the designed di-cationic systems may be viable in the gas phase.

The Chemical Nature of Ti4O10-: Vibrational Predissociation Spectroscopy Combined with Global Structure Optimization.

The gas-phase infrared spectrum of Ti4O10- is studied in the spectral range from 400 cm-1 to 1250 cm-1 using cryogenic ion trap vibrational spectroscopy, in combination with density functional theory (DFT). The infrared photodissociation (IRPD) spectrum of D2-tagged Ti4O10- provides evidence for a structure of lower symmetry that contains a superoxo group (1121 cm-1) and two terminal Ti=O moieties. DFT combined with a genetic algorithm for global structure optimization predicts two isomers which feature a superoxo group: the Cs symmetric global minimum-energy structure and a similar isomer (C1) that is slightly higher in energy. Coupled cluster calculations confirm the relative stability. Comparison of the harmonic DFT spectra (different functionals) with the IRPD spectrum suggests that both of these isomers contribute. Earlier assignments to the adamantane-like C3v isomer with three terminal Ti-O• - groups in a quartet state are not confirmed. They were based on the infrared multiple photon photodissociation (IRMPD) spectrum of bare Ti4O10- and local DFT structure optimizations.

Conformational diversity of 1‑chloro-1-chloromethylsilacyclohexane with experimental (Raman and IR) and computational (DFT, MP2) methods

1‑chloro-1-chloromethylsilacyclohexane (1-Cl-1-ClMSiCH) is a newly synthesized molecular compound whose conformational analysis was performed by means of vibrational spectroscopy and theoretical calculations. Conventional ATR-FTIR and Raman spectroscopic methods were used to obtain vibrational spectra of the liquid sample. Additionally, FTIR spectra of the compound isolated in low-temperature neon and nitrogen matrices were registered to make a complete assignment of the experimental vibrational spectral bands. All theoretically possible 38 canonical ring conformations considering axial/equatorial and cis/trans/gauche-/gauche + positions of the Cl and CH2Cl group were analyzed by utilizing MP2 and B3LYP at aug-cc-pVTZ theory level. The most stable local energy minima were investigated in detail, with the global energy minimum structure being in the chair axial trans conformation. Detailed analysis of the potential energy surface revealed the transition states (TS) and the energy barriers. The conformational path was found to be the chair→ envelope/half-chair (TS)→ skew-boat C1→ boat (TS)→ skew-boat C2. The energy barrier for 1C4 to 1S3 conversion was found to be 4.94 kcal/mol while for the reverse process–it was calculated to be 0.26 kcal/mol. The vibrational analysis and the experimental spectra suggest that the four lowest energy (chair ring) conformers coexist at room temperature. The energy barrier for gauche to trans conversion is 1.15 kcal/mol for axial and 1.04 kcal/mol for equatorial conformers, and it is possible to observe these processes in low-temperature matrices.

Atomic Clusters: Structure, Reactivity, Bonding, and Dynamics.

Atomic clusters lie somewhere in between isolated atoms and extended solids with distinctly different reactivity patterns. They are known to be useful as catalysts facilitating several reactions of industrial importance. Various machine learning based techniques have been adopted in generating their global minimum energy structures. Bond-stretch isomerism, aromatic stabilization, Rener-Teller effect, improved superhalogen/superalkali properties, and electride characteristics are some of the hallmarks of these clusters. Different all-metal and nonmetal clusters exhibit a variety of aromatic characteristics. Some of these clusters are dynamically stable as exemplified through their fluxional behavior. Several of these cluster cavitands are found to be agents for effective confinement. The confined media cause drastic changes in bonding, reactivity, and other properties, for example, bonding between two noble gas atoms, and remarkable acceleration in the rate of a chemical reaction under confinement. They have potential to be good hydrogen storage materials and also to activate small molecules for various purposes. Many atomic clusters show exceptional opto-electronic, magnetic, and nonlinear optical properties. In this Review article, we intend to highlight all these aspects.

Growth of rare gases on coronene

We study the growth of rare gases (Rg) Ne, Ar and Kr on coronene (Cor) molecules, Cor-(Rg)\(_N\). The study is taken up to sizes N=60, and we show the global energy minima for those clusters. Improved Lennard-Jones and atom-bond potentials are used to represent the Rg-Rg and Rg-Cor interactions, respectively. The Basin-Hopping (BH) global optimization technique is employed to locate the putative global energy minimum structures. Results are presented for Cor-(Ne), Cor-(Ar) and Cor-(Kr) systems. Both classical Cor-(Ar)\(_N\) and Cor-(Kr)\(_N\) clusters present the same “magic numbers” for N=3, 6, 10, 14, 19 and 38. This last number marks the first layer of solvation. For Cor-(Ne)\(_N\) clusters, we consider quantum effects adding the zero-point energy (ZPE) into the classical potential energy minima (BH-ZPE). This semiclassical approximation is compared with quantum diffusion Monte Carlo (DMC) calculations up to N=20, obtaining a good agreement and showing that this approximation works reasonably well. In this BH-ZPE approach, high stability configurations for Cor-(Ne)\(_N\) clusters are obtained at N=6, 14, 42, 51 and 57. However, we have not found any evidence of a first solvation layer using either the semiclassical BH-ZPE or the classical BH one.