Stable Isomer Research Articles

Stereochemical Shape Morphing in Diels-Alder Polymer Networks.

The intrinsic reversibility of dynamic covalent bonding, such as the furan-maleimide Diels-Alder (DA) cycloaddition reactions, enables reprocessable, self-healing polymer materials that can be reconfigured via the mechanism of solid-state plasticity. In this work, the temperature-dependent exchange rates of stereochemically distinct endo and exo DA bonds are leveraged to achieve tunable, temperature- and stress-activated shape morphing in Diels-Alder polymer (DAP) networks. Through thermal annealing, ≈35% of endo DA isomers are converted in neat DAP networks to the thermodynamically favored exo form, achieving ≈97% exo after complete annealing at 60°C. This conversion results in a ≈1.7 fold increase in elastic modulus, from 1.7 to 3.0MPa, and significantly alters the stress relaxation and shape recovery behavior. Spatially resolved annealing, is further showcased enabling the precise control of spatial distributions of endo and exo DA bonds across planar geometries. The locally distinct concentrations of endo/exo isomers, achieved by temperature-induced conversion of endo DA isomers to the thermodynamically stable exo DA isomers, gave rise to the spatial distributions of stress relaxation rates and elastic strain recovery mismatch to enable controlled stereochemical shape morphing. This approach provides a simplified, thermally driven method for shape morphing, with potential applications in soft robotics and flexible electronics.

Consecutive Trifluoromethylation of C88(7) Fullerene: A Theoretical Study

AbstractThe trifluoromethylation of C88(7) fullerene has been systematically studied using an energy‐controlled consecutive CF3 addition approach. The thermodynamically favored C88(7)(CF3)2n isomers with 2n = 2–20 were predicted at the DFT B3LYP‐D3BJ/6–311G* level of theory for the first time, in harmony with the two experimentally characterized isomers C88(7)(CF3)12/16. It was found that these stable isomers are formed mainly by 1,4‐additions of CF3 groups, and meanwhile, there are a few stable isomers with isolated CF3 groups for 2n ≤ 12, with ortho addition for 2n > 12, and with triple‐hexagon‐junction addition for the highest degree of trifluoromethylation (2n ≥ 18). The addition patterns of CF3 groups were discussed in terms of the local structural motif of the pristine cage and the formation of stabilizing substructures of local aromaticity. The possible trifluoromethylation pathways of C88(7) were proposed on the basis of the relative Gibbs free energies. The results show that almost all the intermediate isomers for the thermodynamically most stable isomers of C88(7)(CF3)2n possess low relative Gibbs free energies (below 14 kJ·mol−1). Moreover, the hardness, chemical potential, electrophilicity index, electron affinity, HOMO and LUMO energies, and HOMO–LUMO gaps of the thermodynamically most stable C88(7)(CF3)2n isomers were also calculated.

Evolution of Chemistry in the envelope of HOt CorinoS (ECHOS). II. The puzzling chemistry of isomers as revealed by the HNCS/HSCN ratio

The observational detection of some metastable isomers in the interstellar medium with abundances comparable to those of the most stable isomer, or even when the stable isomer is not detected, highlights the importance of non-equilibrium chemistry. This challenges our understanding of the interstellar chemistry and shows the need to study isomeric forms of molecular species to constrain chemical processes occurring in the interstellar medium. Our goal is to study the chemistry of isomers through the sulphur isomer pair HNCS and HSCN, since HSCN has been observed in regions where its stable isomer has not been detected, and the observed HNCS/HSCN ratio seems to significantly vary from cold to warm regions. We used the Nautilus time-dependent gas-grain chemical code to model the formation and destruction paths of HNCS and HSCN in different astrochemical scenarios, as well as the time evolution of the HNCS/HSCN ratio. We also analysed the influence of the environmental conditions on their chemical abundances. We present an observational detection of the metastable isomer HSCN in the Class I object B1-a ($N$=(1.1pm 0.6)times 1012 cm$^ $), but not of the stable isomer HNCS, despite HNCS lying 3200 K lower in energy than HSCN. Our theoretical results show an HNCS/HSCN ratio sensitive to the gas temperature and the evolutionary time, with the highest values obtained at early stages ($t$lesssim 10$^4$ yr) and low ($T_ g $lesssim 20 K) temperatures. A more detailed analysis also shows that the main mechanism forming HNCS in young ($t$$<$10$^5$ yr) and cold ($T_ g $$=$10 K) objects at moderate-low densities ($n$$_ H $leq 10$^5$ cm$^ $) is a grain surface reaction (the chemical desorption reaction N$_ solid $+HCS$_ solid $rightarrow HNCS), unlike previous predictions that suggest only gas-phase chemistry for its formation. However, for the formation of its metastable isomer HSCN, over the same time range and physical conditions, we find that both surface and gas-phase reactions (through the ion H$_2$NCS$^+$) play important roles. In warmer ($T_ g $geq 50 K) regions, the formation of this isomer pair is only dominated by gas-phase chemistry through the ions H$_2$NCS$^+$ (mainly at low densities) and HNCSH$^+$ (mainly at high densities). The results suggest a different efficiency of the isomerisation processes depending on the source temperature. The progressive decrease of HNCS/HSCN with gas temperature at early evolutionary times derived from our theoretical results indicates that this ratio may be used as a tracer of cold young objects. This work also demonstrates the key role of grain surface chemistry in the formation of the isomer pair HNCS and HSCN in cold regions, as well as the importance of the ions H$_2$NCS$^+$ and HNCSH$^+$ in warm/hot regions. Since most of the interstellar regions where HSCN is detected are cold regions (starless cores, Class 0/I objects), a larger sample including sources characterised by high temperatures (e.g. hot cores) are needed to corroborate the theoretical results.

Azobenzene-Attached (NHC)Gold(I) and (NHC)Copper(I) Complexes as Photoswitchable Catalysts.

Photoswitchable (pre)catalysts, N,N'-bis-azobenzene-based (NHC)gold(I) and N,N'-bis-azobenzene-derived (NHC)copper(I) complexes are reported. Trans to cis isomerization of the attached photoswitchable moieties in the Au(I) complex enables four-fold decrement in the rate of oxazoline formation reaction. Whereas the progress of the copper(I) catalyzed, azide-alkyne cycloaddition reaction gets reduced by at least threefold. Alternate exposure to UV and blue light could easily toggle the rate of reactions remotely. The catalytic activity of thermodynamically stable trans-trans isomers is found to be similar to the common N-aryl substituted NHC-Au/Cu(I) complexes. NHC-Au(I) and -Cu(I) compounds bearing (trans)azobenzene moieties were characterized by X-ray diffraction. Photoswitching, recyclability studies, and the metastable isomer's thermal half-life in both complexes were studied via UV-visible spectroscopy. Whereas the extent of photoswitching and concomitant formation of geometrical isomers were investigated by using 1H-NMR spectroscopic study. Calculated percentage buried volumes of the three geometrical isomers show the trend trans-trans<trans-cis<cis-cis.

Experimental Elucidation of a Cubane Water Cluster in the Hydrophobic Cavity of UiO-66.

Nanoscale water plays a pivotal role in determining the properties and functionalities of materials, and the precise control of its quantity and atomic-scale ordered structure is a focal point in nanotechnology and chemistry. Several studies have theoretically discussed the nano-ordered ice within one- or two-dimensional space and without confinement through hydrogen bonds. In particular, the water cluster has been predicted to play a significant role in biomolecules or functional nanomaterials; however, there has been little experimental evidence for their presence in hydrophobic cavities. In this study, the cubane water octamer - the most stable isomer among small water clusters - was detected within the hydrophobic cavities of UiO-66 metal-organic frameworks, revealing the presence of the smallest ice in their hydrophobic cavity, in the absence of hydrogen bonding. This observation contrasts earlier examples of water clusters confined within nanocavities through hydrogen bonds and provides experimental evidence for water-cluster capturing within hydrophobic cavities. Consequently, our renewed understanding of hydrophilicity and hydrophobicity warrants a design re-evaluation of materials for chemical applications, including fuel cells, water harvesting, catalysts, and batteries.

Stereodivergent atom transfer radical addition of α-functionalized alkyl iodides to alkynes: a strategy for selective synthesis of both E- and Z-iodoalkenes.

The geometrical control of atom transfer radical addition (ATRA) reactions to alkynes poses significant challenges. Herein, we present a uniform solution by developing a stereodivergent synthetic method for both isomers of the resulting alkene products, starting from the same materials. The synthesis of the thermodynamically more stable isomer utilizes the strategy of uphill catalysis while the accumulation of the less stable isomer is facilitated by a manganese-catalyzed iodo-abstraction/radical rebound process, taking advantage of its reversibility. Various substituted alkyl iodides can be used to provide easy access to both isomers of iodoalkene products with valuable functional groups such as CF3, CF2H, CN, ester, or amide at the allylic position.

Effects of sulfation on the flotation capacity of oleic acid in the dolomite and fluorapatite system: A combined experimental and DFT study

Dolomite cannot be efficiently separated from fluorapatite (FA) by oleic acid in an acidic slurry, due to the poor collecting ability of oleic acid. In this work, sulfation was used to improve the flotation performance of oleic acid. Flotation tests showed that the sulfating collector exhibited stronger flotation ability for dolomite. However, the H2SO4-treated FA could not be floated by the sulfating collector. The solubility of the sulfating collector at pH 4.5 was higher than that of HOL at the same pH. Thus, more sulfating molecules and anions were generated in the collector solution, which accounted for the high flotation efficiency of the sulfating reagent. The sulfating collector molecule and anion could adsorb on the H2SO4-treated dolomite surface. Moreover, the reaction of the sulfating collector anions with the dolomite surface generated alkyl Mg/Ca salts.Furthermore, DFT calculations were employed to evaluate the interactions of the sulfating reagent with the H2SO4-treated dolomite surface. The sulfation produced two isomers. The most stable isomer, i.e., 10-sulfooxy stearic acid (SOA), was used in the calculations. The SOA anion could vertically or paralelly adsorb onto the dolomite. The parallel structure was more stable, where the COO− and OSO3− groups of SOA anion bonded with two metal atoms on the dolomite surface. These findings suggest that the sulfation collector is suitable for the reverse flotation of collophane.

The Chemistry and Biological Effects of Fused 1,2,4-triazolo[4,3-c]pyrimidines and their Isomeric 1,2,4-triazolo[1,5-c]pyrimidines

Concerning polycyclic heterocyclic compounds, fused triazolopyrimidines and their substituted analogs have been studied recently from a chemical and biological point of view. Triazolopyrimidines have eight different positional isomers based on their structural arrangement and nitrogen atom positions. The present review concerns synthesizing 1,2,4- triazolo[4,3-c]pyrimidines and 1,2,4-triazolo[1,5-c]pyrimidines fused with a fivemembered ring containing one heteroatom. The 1,2,4-triazolo[4,3-c]pyrimidines can be prepared by closing the triazole ring on the 4-hydrazinopyrimidine ring, and the 1,2,4- triazolo[1,5-c]pyrimidines can be prepared by closing the triazole ring on the 4- iminopyrimidine-3-amine ring. The transformation of 1,2,4-triazolo[4,3-c]pyrimidine to the more thermodynamically stable isomer triazolo[1,5-c]pyrimidine derivatives via Dimroth rearrangement under different reaction conditions is also discussed. Moreover, the biological activity of both series is presented.

Schleyer hyperconjugative aromaticity in indene scaffolds

In the present research, the Schleyer hyperconjugative aromaticity was used to enhance the aromaticity of indene scaffolds. The first section of the research focused on examining the thermodynamic stability and electronic characteristics of the four structural isomers of indene. Results indicate that 1H-indene scaffolds are the most stable thermodynamic isomers of indene derivatives exceeding 100 kJ/mol. The hierarchy of stability is as follows: 1H-indenes > 2H-indenes > 5H-indenes > 4H-indenes. The aromaticity of 5- and 6-membered rings in the isomeric structures was investigated using the B3LYP/6–311 + G(d,p) method in the second section of the study. The hyperconjugative aromaticity of 5MR and 6MR was assessed using the harmonic oscillator model of aromaticity index, Bird index, Shannon index, aromatic fluctuation index, and the nucleus independent chemical shift. The results reveal that introducing electron-donating groups on 6MR enhances the aromaticity of 5MR. Moreover, adding two fluorine atoms on the Csp3 site negatively affects the aromaticity and induces antiaromaticity in the indene scaffold. Based on aromaticity data, the order of increasing aromaticity in the presence of different groups is F < CH3 < H < SiH3 < GeH3 < Si(CH3)3 < Ge(CH3)3. The extent of the Schleyer hyperconjugation interaction was also quantified using the E(2) parameter obtained from the NBO calculations.

2-(1,1-Dicyanomethylene)rhodanine-Functionalized Oligothiophenes: A Structure-Property Investigation of Z/E Photoisomerization Behavior.

A series of oligothiophenes singly and doubly functionalized with dicyanorhodanine (RCN) units have been investigated to understand their Z/E photoisomerization behavior upon structural modulation. Monotopic RCN target molecules (1-Z-9-Z) were designed to observe the consequences of π-conjugation, solubilizing group substitution, and formylation of the thiophene units. In all cases, the Z isomer is obtained from synthesis as the thermodynamically stable isomer, whereas the E isomer is achieved through selective irradiation (including red light, λirr = 628 nm) as a Z/E mixture in solution. For the quarterthiophene entries, photoisomerization is inhibited, with photoirradiation resulting only in degradation. The result comports with concentration-dependent studies, which show that increasing π-conjugation results in greater aggregation and muted Z/E photoisomerization. Ditopic RCN targets (10-ZZ-12-ZZ), mimicking acceptor-donor-acceptor (A-D-A) oligomers relevant to OPV materials, also show evidence of photoisomerization in solution, with formation of Z,Z/Z,E mixtures at the photostationary state (PSS). Complementary ground- and excited-state DFT calculations show excellent agreement with the experimental findings. This comprehensive structure-property analysis is expected to both guide and caution the functional materials community with respect to the usage of photoisomerizable RCN-oligothiophenes for optoelectronic applications.

Evolutionary Pathways of T-Phase Transition Metal Dichalcogenides: A Comprehensive Study of PtxSey Clusters.

Understanding the transition from nonplanar to planar clusters is crucial for the controllable synthesis of transition metal dichalcogenide (TMDC) monolayers. Using PtSe2 as a model, we investigate how the chemical environment influences the nucleation and growth stages of monolayer PtSe2 through structure searching and first-principles calculations. We established a comprehensive database of platinum selenide clusters (PtxSey, x = 1-10), analyzing 2095 unique clusters and identifying 191 stable isomers and 63 structures with the lowest formation energy on the convex hull. Our findings reveal a chemical environment-dependent phase transition from 3D structures to the planar T-phase of PtxSey clusters, representing an evolutionary route for PtSe2 growth. Clusters such as PtSe6, Pt2Se9, Pt3Se10, and Pt7Se10 in Pt-rich environments, as well as Pt2Se15 and Pt10Se32 in Se-rich environments, have been found to exhibit high stability. Additionally, the impact of varying chemical potentials of Pt and Se on the stability of these clusters is explored. PtSe4 and PtSe6 are found to be highly stable under most experimentally achievable chemical potential conditions and may serve as dominant precursors during PtSe2 growth. This work advances our understanding of the nucleation processes of PtSe2 and other T-phase TMDC materials.

Strongly bound anions featuring bismuth fluoride building blocks

The stability of polynuclear superhalogen anions composed of BiF5 building blocks was investigated using ab initio electronic structure methods and flexible basis sets. A comprehensive exploration of the ground state potential energy surfaces of (Bi2F11)−, (Bi3F16)− and (Bi4F21)− anions, which can be viewed as comprising BiF5 fragments and an additional fluorine atom, led to the identification of their isomeric structures. It was found that the most stable isomers, predicted to dominate at room temperature, correspond to chain-like extended structures containing BiF6 subunits, with fluorine ligands arranged octahedrally around Bi atoms, sharing F atoms to form Bi–F–Bi bridging linkages. The vertical electron detachment energies of the (BinF5n+1)− anions (n = 1–4) were found to be very high (ranging from 10.91 to 13.36 eV) and increased with the number of bismuth atoms (n) and thus the BiF5 building blocks involved in the structure. Thermodynamic stability of the (BinF5n+1)− anions (i.e., their susceptibility to fragmentation) was also verified and discussed.

LoGAN: local generative adversarial network for novel structure prediction

Abstract The efficient generation and filtering of candidate structures for new materials is becoming increasingly important as starting points for computational studies. In this work, we introduce an approach to Wasserstein generative adversarial networks for predicting unique crystal and molecular structures. Leveraging translation- and rotation-invariant atom-centered local descriptors addresses some of the major challenges faced by similar methods. Our models require only small sets of known structures as training data. Furthermore, the approach is able to generate both non-periodic and periodic structures based on local coordination. We showcase the data efficiency and versatility of the approach by recovering all stable C5H12O isomers using only 39 C4H10O and C6H14O training examples, as well as a few randomly selected known low-energy SiO2 crystal structures utilizing only 167 training examples of other SiO2 crystal structures. We also introduce a filtration technique to reduce the computational cost of subsequent characterization steps by selecting samples from unique basins on the potential energy surface, which allows to minimize the number of geometry relaxations needed after structure generation. The present method thus represents a new, versatile approach to generative modeling of crystal and molecular structures in the low-data regime, and is available as open-source.

Insights into the adsorption of thiophene and fluorinated-thiophenes on the Mg4O4 cluster: a quantum chemical investigation

In this work, the adsorption of thiophene on the Mg4O4 cluster was examined at the LC-ωPBE/6-311G(d,p) level of theory. The influence of replacing hydrogen atoms of thiophene with fluorine atoms was considered. The comparison of relative stabilities of possible isomers indicated most stable isomers were 3-FT … Mg4O4, 3,4-DFT … Mg4O4, 2,3,4-TFT … Mg4O4 structures in the mono, di and tri-fluorinated thiophenes, respectively. Corrected adsorption energy and thermodynamic parameter values of these systems were evaluated and the substituent effect on the adsorption was explored. 2-FT … Mg4O4, 3,4-DFT … Mg4O4, 2,3,4-TFT … Mg4O4 structures indicated the most significant adsorptions in the mono, di and tri-fluorinated thiophenes, respectively. Electrophilicity-based charge transfer (ECT) was employed to illustrate charge transfer between aromatic systems and the Mg4O4 cluster. Quantum theory of atoms in molecule (QTAIM) and interaction region indicator (IRI) were used to deeply investigate two fragments.

Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects.

Among azobenzene derivatives, azothiophenes represent a relatively recent family of compounds that exhibit similar characteristics as dyes and photoreactive systems. Their technological applications are extensive thanks to the additional design flexibility conferred by the heteroaromatic ring. In this study, we present a comprehensive investigation of the structural and electronic properties of novel dyes derived from 3-thiophenamine, utilizing a multilevel approach. We thoroughly examined the potential energy surfaces of the E and Z isomers for three molecules, each bearing different substituents on the phenyl ring at the para position relative to the diazo group. This exploration was conducted through quantum chemistry calculations at various levels of theory, employing a continuum solvent model. Subsequently, we incorporated an explicit solvent (a dimethyl sulfoxide-water mixture) to simulate the most stable isomers using classical molecular dynamics, delivering a clear picture of the local solvation structure and intermolecular interactions. Finally, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was employed to accurately describe the evolution of the solutes' properties within their environment, accounting for finite temperature effects.

Kekulé Counts, Clar Numbers, and ZZ Polynomials for All Isomers of (5,6)-Fullerenes C52-C70.

We report an extensive tabulation of several important topological invariants for all the isomers of carbon (5,6)-fullerenes Cn with n = 52-70. The topological invariants (including Kekulé count, Clar count, and Clar number) are computed and reported in the form of the corresponding Zhang-Zhang (ZZ) polynomials. The ZZ polynomials appear to be distinct for each isomer cage, providing a unique label that allows for differentiation between various isomers. Several chemical applications of the computed invariants are reported. The results suggest rather weak correlation between the Kekulé count, Clar count, Clar number invariants, and isomer stability, calling into doubt the predictive power of these topological invariants in discriminating the most stable isomer of a given fullerene. The only exception is the Clar count/Kekulé count ratio, which seems to be the most important diagnostic discovered from our analysis. Stronger correlations are detected between Pauling bond orders computed from Kekulé structures (or Clar covers) and the corresponding equilibrium bond lengths determined from the optimized DFTB geometries of all 30,579 isomers of C20-C70.

Energy and spectroscopic parameters of neutral and cations isomers of the CnH2 (n = 2-6) families using high-level ab-initio approaches.

Cationic species, previously detected from ion-induced desorption of solid methane by plasma desorption mass spectrometry (PDMS), and neutral species, are investigated using high-level ab-initio approaches. From a set of 25 cationic and 26 neutral structures belonging to CnH2 (n = 2-6) families, it was obtained the energy, rotational constants, harmonic vibrational frequency, charge distribution and excitation energies. The ZPVE-corrected energies, at CCSD(T)-F12; CCSD(T)-F12/RI/(cc-pVTZ-F12, cc-pVTZ-F12-CABS, cc-pVQZ/C) (n = 2-5) and CCSD(T)/cc-pVTZ (n = 6) levels, reveal that the topology of the most stable isomer vary with n and the charge. Out of 674 harmonic frequencies, those with maximum intensity are generally in the 3000-3500 cm-1 range. Analysis of 169 vertical transition energies calculated with the EOM-CCSD approach, suggest three C6H2 species as potential carriers of the diffuse interstellar bands (DIB). Systematic comparison of properties between neutral and cationic species can assist in the structural description of complex matrices.

In Quest of the Missing C2H6O2 Isomers in the Interstellar Medium: A Theoretical Search.

Ethylene glycol (C2H6O2), the only diol detected in the interstellar medium (ISM), is a key component in the synthesis of prebiotic sugars. Its structural isomer, methoxymethanol, has also been found in the ISM. Our results show that neither ethylene glycol (ethane-1,2-diol) nor methoxymethanol is the most stable isomer. Using high-level computational methods, we identified five isomers: two diols, one hydroxy ether, and two peroxides. The geminal diol 1,1-ethanediol (ethane-1,1-diol) is the most stable isomer, although it has not been detected in the ISM, whereas the two peroxides are less stable than the geminal diol by 60 kcal/mol. This study also provides the rotational constants and dipole moment for each conformer of every C2H6O2 isomer.

(Invited) Machine Learned Potential for Fullerenes Based on Continuous-Filter Convolutional Neural Network

We trained a convolutional neural network (CNN) to quickly and accurately reproduce energies, forces and dipole moments calculated by density functional theory (DFT) for fullerenes ranging from C20 to C80. The obtained reproduction errors per atom are about 0.001 Hartree for energies, 0.0003 Hartree/Bohr for forces and 0.001 Debye for dipole moments. The speedup of calculations with respect to DFT/6-31G is about 105 (for CPU), when using graphics processing unit (GPU) about 106. The obtained machine learned potential (MLP) can be used, for example, for a fast screening of the most stable fullerene isomers.

Solvent effects on the structures of the hydrated copper dication clusters

Understanding the solvation process requires an understanding of how the solvent affects the molecular cluster configurations. The current study examined the impact of solvents on the structures of the hydrated Cu2+ cation, as well as the temperature dependence, and the energetics of the hydrated Cu2+ cation clusters from sizes n=1 from n=10 (Cu2+(H2O)n=1−10). The potential energy surfaces (PESs) in the solvent phase (represented by a dielectric continuum medium) at the MP2/6-31++G(d,p) level of computation have been comprehensively investigated. We employed the integral equation formalism polarized continuum model (IEF-PCM) to describe the dielectric continuum medium. It is pointed out that changes in PESs of hydrated copper dication isomers and structural morphologies occur in the continuum medium. Thus, the relative energies are smallest at T=0 K and for the cluster populations of Cu2+(H2O)n=1−10 are modified. Thus, in the solvent phase, the competition between the conformers is more severe than in the gas phase. Furthermore, highly coordinated conformers are more favorable, and favored conformers in the gas phase are disfavored in the solvent phase. The structural investigations are validated by the analysis of Wiberg Bond Index (WBI) at 300 K. In the solvent phase, the WBIs of the most stable isomers are the smallest and the WBIs of axial bonds are lower than those of equatorial bonds. Concerning the energy analysis, the binding energies were predicted for enormous sizes (at saturation) using a fit function. Thus, the new values of the binding energies obtained are -5467.8 and ▪ in the gas and solvent phases respectively. All these observed differences are due to the effects of the implicit solvent.