Stabilities Of Different Isomers Research Articles

Inorganic Polysulfides in Solution: Structural Properties and Conformational Isomerism.

We present a comprehensive theoretical examination of the structural properties of dianionic polysulfides [Sn]2- (n = 2-6), their conjugated monoacids [HSn]- (n = 2-6), and a selection of 1e--oxidized radical anions [Sn]•- (n = 2-4), in aqueous and dimethyl sulfoxide (DMSO) solutions. We investigated the structures and stabilities of various conformational isomers within these families of compounds by employing Quantum Mechanics-Molecular Mechanics (QM-MM) Molecular Dynamics (MD) simulations. The explicit inclusion of solvent molecules in the calculations revealed stable conformational structures that were previously unreported and might have appreciable concentrations in real systems. The interconversions between the isomeric structures proceed on the order of hundreds of picoseconds and are energetically similar to the isomerization processes in substituted cyclohexanes. We also conducted a detailed analysis of the stability of different isomers of the radical anion [S4]•- in solution. Our findings highlight the significant influence of the solvent on the isomerizations, a result that could be particularly relevant for enhancing the performance of metal-sulfur batteries.

Solvation energies of ferrous ion in methanol at various temperatures

• Solvated ferrous ion in methanol is hexa-coordinated. • Accurate free energy and enthalpy of the solvated ferrous ion in methanol available. • Binding and clustering energies of the solvated ferrous ion in methanol available. The accurate determination of the solvation free energies or solvation enthalpies of ferrous ion in a given medium is subject to the determination of the most favored structures of the ferrous ion in this medium. In this work, we investigated structures, relative stabilities, clustering energies, binding energies, solvation enthalpies and solvation free energies of the ferrous ion in methanol for temperatures ranging from 20 K to 400 K. It is pointed out that the coordination number of the solvated ferrous ion in methanol is six, but could decrease slightly when the temperature increases. The temperature dependence of the relative stability of different isomers obtained proves that, for T ranging from 20 K to 400 K, the population is dominated by one structure and we noted the presence of fourfold coordinated structures for n > 6. Solvation energies of ferrous ion in methanol were computed following an hybrid solvation scheme. Finally, the solvation free energy of ferrous ion in methanol at room temperature (298.15 K), is −2066.1 kJ mol −1 and the corresponding solvation enthalpy is −2103.5 kJ mol −1 . Taking into account the temperature effects, the solvation free energies are more affected by the change of temperature mainly for temperature higher than 200 K. However, the effect of temperature is insignificant on the solvation enthalpies. At the saturation, the binding electronic energy per methanol molecule, the binding enthalpy per methanol molecule and the binding free energy per methanol molecule of the solvated ferrous ion in methanol are −142.1, −140.3 and −104.0 kJ mol −1 , respectively. For the clustering energies, we reported −6.9, −6.8 and -3.4 kJ mol −1 corresponding respectively to the clustering electronic energy, the clustering enthalpy and the clustering free energy of the solvated ferrous ion in methanol.

Hydrogen adsorption and storage on palladium-functionalized C20 bowl and C20H10 bowl molecule including hydrogen saturation

This study investigated hydrogen molecule adsorbing on palladium-functionalized C20 bowl and its H-saturated form (C20H10 bowl) using the B3LYP-D3 model. Moreover, this study examined the stability of different isomers of hydrogen adsorption. The values of adsorption energy were calculated in the investigated systems. This study demonstrated changes in the dipole moment and structural parameters. Additionally, this study indicated the differences in the frontier orbital energy and HOMO—LUMO gap values. Electrophilicity-based charge transfer showed charge transfer between fragments. Furthermore, this study also computed the hydrogen molecule's recovery duration in the investigated systems. In addition, the present study showed the field emission features of the examined system.

On the strength of hydrogen bonding within water clusters on the coordination limit.

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18, 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice Ih ). The strongest HBs within H2 O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H2 O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H2 O clusters.

Novel geochemical proxies derived from 1D simulation of Liaohe oil sand bitumen to monitor in-situ combustion process

1-D combustion tube in-situ combustion (ISC) simulation experiment has been performed on a natural bitumen bearing core. Five ISC zones were distinguished on the basis of the temperature filed and oil saturation analysis of the experiment. A suite of six oil sand residues at different locations after ISC simulation (initial, oil bank, condensation, coking, combustion zone and burned zone, respectively) were obtained for further analysis by using gas chromatography-mass spectrometry to assess the ISC impact and possible proxies monitoring the ISC process. Compounds in the saturated and aromatic hydrocarbon fractions change systematically with increasing temperatures. The concentrations of various compound classes increase generally from the initial zone to the combustion zone, then decrease drastically in the burned zone. However, different compounds show distinct behaviors during ISC and several geochemical proxies were temporary proposed. The amount of light molecular weighted n-alkanes increases significantly, while isoprenoids and heavy molecular weighted n-alkanes show the same trend but less dramatic changes. The ratios of n-C17/pristane (Pr) and n-C18/pyhtane (Ph) and ∑n-C20−/∑n-C20+ increase continuously from the initial zone to the combustion zone and clearly reflect ISC impact. A similar proxy can be derived from the ratio of summed n-alkanes to summed pentacyclic terpanes (∑n-alkanes/∑PTs), which increase more perceptibly due to easy decomposition of biomarkers. In the aromatic fraction, the most sensitive proxy to monitor ISC is derived from degree of alkylation of aromatic homologues. Non-substituted compounds especially naphthalene and phenanthrene increase constantly from the initial zone to the burned zone accompanied by the depletion of highly alkylated counterparts. Some newly formed compounds such as 2-methylanthracene and benz[a]anthracene are defined combustion evidence. However, commonly used maturity parameters based on relative stability of different isomers show no significant variation and cannot serve as valid ISC proxies.

Characterization of Molybdenum Dithiocarbamates by First-Principles Calculations.

Molybdenum dithiocarbamate (MoDTC) is a well-known lubricant additive, which, in tribological conditions, is capable of forming layers of MoS2 with excellent friction reduction properties. Despite being widely employed in commercial engine oils, a comprehensive theoretical description of the properties of MoDTC is still lacking. In this work, we employ density functional theory to study the structural, electronic, and vibrational properties of MoDTC. We investigate the relative stability of different isomers, different hydrocarbon terminations, and oxidized complexes. Oxidation was found to be energetically favorable for a wide range of conditions, and the most favorable position for oxygen atoms in MoDTC turned out to be the ligand position. These results, along with the calculated reaction energies for different dissociation paths, can be useful to better identify the elementary steps of the decomposition process of MoDTC.

Isomeric Equilibria, Nuclear Quantum Effects, and Vibrational Spectra of M+(H2O) n=1-3 Clusters, with M = Li, Na, K, Rb, and Cs, through Many-Body Representations.

A quantitative characterization of the molecular mechanisms that regulate ion solvation is key to the microscopic understanding of fundamental processes taking place in aqueous environments with major implications for different fields, from atmospheric chemistry to materials research and biochemistry. This study presents a systematic analysis of isomeric equilibria for small M+(H2O) n clusters, with M = Li, Na, K, Rb, and Cs, from 0 to 200 K. To determine the relative stability of different isomers of each M+(H2O) n cluster as a function of temperature, replica exchange simulations are carried out at both classical and quantum levels with the recently developed many-body MB-nrg potential energy functions, which have been shown to exhibit chemical accuracy. Anharmonic vibrational spectra are then calculated within the local monomer approximation and found to be in agreement with the available experimental data, providing further support for the accuracy of the MB-nrg potential energy functions. The present analysis indicates that nuclear quantum effects become increasingly important for larger M+(H2O) n clusters containing the heavier alkali metal ions, which is explained in terms of competing ion-water and water-water interactions along with the interplay between energetic and entropic effects. By directly connecting experimental measurements with molecular properties calculated at the quantum mechanical level, this study represents a further step toward the development of a consistent picture of ion hydration from the gas to the condensed phase.

Influence of polyether chain on the non-covalent interactions and stability of the conformers of calix[4]crown ethers

Conformational preferences of the calix[4]crown-(4,5,6,7)-ethers were studied utilizing HF/6-31G(d), B3LYP/6-31G(d), B3LYP/6-311G(d), MPWB95/6-31G(d), MPWIPW91/6-31G(d) and M062X/6-31G(d) methods. DFT-D3 (Becke–Johnson) dispersion correction method was also employed. The results acquired from the analysis of the computational data indicated that the stability of conformers of calix[4]crown-(4,5,6,7)-ethers follows the order; cone conformer > partial cone conformer > 1,3-alternate conformer. It was initially assessed, in general, that both hydrogen bond and OH⋯π interactions play a crucial role in determining the stability of the different conformers. It was further observed that the strength of both H-bond and OH⋯π interactions, are dependent on the length of the polyether bridge. Hence, in order to comprehend them better, the effect of these interactions was studied systematically on the conformational stability of different isomers. It is found that both intramolecular hydrogen bonds and O–H⋯π interactions are mainly responsible for relative stabilities of these conformers, which in turn is also dependent on the length of the polyether bridges. The computational study reported here demonstrate that the size of the polyether bridge along with non-covalent interactions such as hydrogen bond and OH⋯π interactions play an important role in determining the stability of the conformers of calix[4]crown ethers.

Dibenzothiophenes and benzonaphthothiophenes in oils, and their application in identifying oil filling pathways in Eocene lacustrine clastic reservoirs in the Beibuwan Basin, South China Sea

Dibenzothiophenes (DBTs) and benzo[b]naphthothiophenes (BNTs) are important sulfur heterocyclic aromatic compounds in oils and sedimentary rock extracts. Based on both migration fractionation effects and differences in thermal stability of different isomers, DBTs and BNTs can be used to trace oil migration orientations and filling pathways. They are present in significant abundances in oils, including light oils and condensates, in which biomarkers are commonly absent or present only in extremely low concentrations. Molecular biomarker compositions indicate that all oils and condensates in the Eocene clastic reservoir of the Fushan Depression (Beibuwan Basin, South China Sea) belong to a single oil population. In this study, three geochemical indicators relating to DBTs and BNTs, namely; (1), 4-/1-methyldibenzothiophene (4-/1-MDBT); (2), total content of DBTs; and (3), benzo[b]naphtha[2,1-d]thiophene/(benzo[b]naphtha[2,1-d]thiophene+benzo[b]naphtho[1,2-d]thiophene) ([1,2]BNT/([1,2]BNT+[1,2]BNT)) were applied to trace oil migration orientations and filling pathways. The results show that these parameter values gradually decrease from northeast to southwest, towards the Huachang Uplift, and from north to south towards the Bailian Faulted-Belts. Therefore, the source kitchen for identified oil accumulations in the Huachang Uplift is likely to be located in the Bailian Sag, which lies to the northeast of the Huachang Uplift. Zones in the Bailian Sag, situated upstream of the preferred oil filling pathways are likely to be the most favorable prospecting regions. It is concluded that relative parameters of DBTs and BNTs are practical molecular indicators for tracing oil migration orientations and filling pathways.

Understanding the Boron-Nitrogen Interaction and Its Possible Implications in Drug Design.

2-Aminoethoxydiphenylborate (2-APB) is a broad-spectrum modulator of various membrane proteins. Specifically, it exhibits concentration dependent modulation of calcium signaling through store-operated calcium (SOC) channels: low micromolar concentration of 2-APB stimulates SOC entry while a higher concentration induces complete inhibition. Ab initio quantum chemical calculations show that the relative stability of the two major isomers of 2-APB (cyclic and extended) is about 8 kcal/mol. The dual functionality of 2-APB for SOC channels is thus likely associated with its ability to switch among isomeric forms, suited to different binding sites in the SOC channels with distinct binding affinities. Importantly, the moderate relative stability of different isomers results from a delicate balance between the intramolecular boron-nitrogen coordinate bond with strength about -45 kcal/mol and ring strain engendered by cyclic oligomerization. The synergistic effect of these two factors likely makes 2-APB an ideal dual effect drug.

Formation of Different Isomers of Phosphine–Imidazolyl and –Pyridyl Ruthenium(II) Complexes Affecting the Catalyst Activity in the Acceptorless Dehydrogenation of Alcohols

AbstractThe synthesis, reactivity, and catalytic activity of RuII complexes with different pyridine‐ and imidazole‐based P,N ligands are reported. The investigations reveal a strong influence of the N‐heterocycle and the steric demand of the phosphine groups on the stability of different isomers of [L2RuX2] (L = P,N ligand; X = Cl, H). The imidazole‐based complex 5 with dicyclohexylphosphine groups was found to be the most active precatalyst for the acceptorless dehydrogenation of primary alcohols, whereas different phosphine groups at the imidazole ligand as well as pyridine‐based ligands caused a drop in catalytic activity. In the presence of a primary amine, imines are preferentially formed under these conditions. In summary, the investigations show that comparably small changes in the ligand moiety have a strong effect on the relative stability of stereoisomers for both hydride and chloride complexes, whereas isomerization of the kinetic reaction products was observed in some cases. The described changes in the ligand moiety most probably have a strong impact on the relative stabilities of isomeric intermediates as well and thus affect the catalytic activity of these complexes.

AN ORGANIC COSMO-BAROMETER: DISTINCT PRESSURE AND TEMPERATURE EFFECTS FOR METHYL SUBSTITUTED POLYCYCLIC AROMATIC HYDROCARBONS

There are a number of key structures that can be used to reveal the formation and modification history of organic matter in the cosmos. For instance, the susceptibility of organic matter to heat is well documented and the relative thermal stabilities of different isomers can be used as cosmothermometers. Yet despite being an important variable, no previously recognized organic marker of pressure exists. The absence of a pressure marker is unfortunate considering our ability to effectively recognize extraterrestrial organic structures both remotely and in the laboratory. There are a wide variety of pressures in cosmic settings that could potentially be reflected by organic structures. Therefore, to develop an organic cosmic pressure marker, we have used state-of-the-art diamond anvil cell (DAC) and synchrotron-source Fourier transform infrared (FTIR) spectroscopy to reveal the effects of pressure on the substitution patterns for representatives of the commonly encountered methyl substituted naphthalenes, specifically the dimethylnaphthalenes. Interestingly, although temperature and pressure effects are concordant for many isomers, pressure appears to have the opposite effect to heat on the final molecular architecture of the 1,5-dimethylnaphthalene isomer. Our data suggest the possibility of the first pressure parameter or "cosmo-barometer" (1,5-dimethylnaphthalene/total dimethylnaphthalenes) that can distinguish pressure from thermal effects. Information can be obtained from the new pressure marker either remotely by instrumentation on landers or rovers or directly by laboratory measurement, and its use has relevance for all cases where organic matter, temperature, and pressure interplay in the cosmos.

Quantum chemical studies on the structural and electronic properties of nickel sulphide and iron sulphide nanoclusters

Nanoclusters of nickel sulphide (NiS) n and iron sulphide (FeS) n for n = 3–5 are studied using B3LYP exchange correlation function with 6-31G as a basis set. The structural stability of different isomers of NiS and FeS is analysed with the optimized energy, binding energy and vibrational studies. The electronic properties of isomers are discussed in terms of HOMO–LUMO gap, ionization potential, electron affinity, and embedding energy of different clusters. Based on the calculated energy, planar ring, linear ladder and bipyramidal cube of NiS and FeS nanoclusters are found to be more stable. The increase in number of atoms in the clusters leads to increase in its stability. The dipole moment is high for planar rhombus and linear ladder structures of NiS and FeS nanoclusters. The ionization potential and electron affinity are high for planar ring structure of NiS and FeS clusters. The value of energy gap of linear ladder NiS nanocluster and cube and bipyramidal cube structures of FeS is found to be low. The binding energy for cube structure of NiS and FeS clusters is found to be high. Hexagonal ring structure of NiS and FeS clusters has low embedding energy value. The other parameters such as dipole moment and point symmetry are also discussed. The structural stability and electronic properties will provide an insight for experimentalist to tailor new materials that have potential importance in engineering applications.

Structure and magnetic properties of (Fe2O3)(n) clusters (n = 1-5).

Global minimum structures of neutral (Fe2O3)n clusters with n = 1-5 were determined employing the genetic algorithm in combination with ab initio parameterized interatomic potentials and subsequent refinement at the density functional theory level. Systematic investigations of magnetic configurations of the clusters using a broken symmetry approach reveal antiferromagnetic and ferrimagnetic ground states. Whereas (Fe2O3)n clusters with n = 2-5 contain exclusively Fe(3+), Fe2O3 was found to be a special case formally containing both Fe(2+) and Fe(3+). Calculated magnetic coupling constants revealed predominantly strong antiferromagnetic interactions, which exceed bulk values found in hematite. The precise magnetization (spin) state of the clusters has only small influence on their geometric structure. Starting from n = 4 also the relative energies of different cluster isomers are only weakly influenced by their magnetic configuration. These findings are important for simulations of larger (Fe2O3)n clusters and nanoparticles.

Structural stability, chemical order and reactivity pattern of MopWq clusters, with p + q = 8

The electronic structure and related properties of free-standing MopWq atomic clusters, with p + q = 8, are investigated within the framework of the fully unconstrained version of the density functional theory as implemented in the SIESTA code. Starting from the structures of the lowest-energy isomers of pure Mo8 and W8, they are decorated for any possible homotops and their geometries are re-optimized. Binding energies, excess energies and second differences in binding energies are reported and used to discuss relative stabilities of different isomers. Interatomic distances, magnetic moments, average coordination numbers and order parameters are also reported to achieve a better understanding of the structural evolution of the species when Mo atoms are replaced by W atoms and vice versa. Adiabatic ionization potentials, adiabatic electronic affinities and absolute hardnesses are also shown and discussed in the context of the potential reactivity of MopWq clusters against hydrotreatment processes. Those reactivity indexes suggest that the Mo3W5 aggregate should be a good candidate to take part in a reaction governed by a charge transfer process.

Theoretical study of Rh(I) and Rh(III) bis(isonitrile) complexes as promising reagents for synthesis of N-heterocyclic carbenes

The properties of the [RhCl(PH3)(CNMe)2] and [RhCl3(PH3)(CNMe)2] complexes (relative stability of different isomers, structural features, vibrational frequencies, bond nature, atomic charge distribution, and well as analysis of the MO composition and energies) have been studied by quantum-chemical methods. For the [RhCl(PH3)(CNMe)2] complex, the cis isomer is the most stable one; for the [RhCl3(PH3)(CNMe)2] complex, the cis-mer isomer is the most stable one. In the [RhCl(PH3)(CNMe)2] complex, the moderate π back-donation effect is observed. The coordination of C≡NMe to the metal should lead to activation of the ligand in nucleophilic addition and cycloaddition reactions with a normal electron distribution and hinder the electrophilic attack at the N atom of isonitrile.

Reactions of heterocumulenes with organometallic reagents: XVIII. Quantum-chemical study on the mechanisms of formation of thiophene ring from lithium and potassium buta-2,3-dienimidothioates

Thermodynamic stabilities of different isomers and tautomers of lithium and potassium buta-2,3-dienimidothioates (ambident N,S-centered anionic adducts derived from methoxyallenyl carbanion and methyl isothiocyanate) as real or potential precursors of 3-methoxy-N,N-dimethylthiophen-2-amine were estimated by quantum-chemical calculations in terms of the density functional theory. Gradient channels corresponding to concerted (one-step) and stepwise (two-step) mechanisms of formation of thiophene ring from the most stable conformers and tautomers were localized. The formation of thiophene structure from lithium and potassium buta-2,3-dienimidothioates in two steps via intramolecular cyclization to thiophen-2(5H)-ylidene anion and its isomerization into thienylamide was found to be more probable. The activation barriers in both stepwise and concerted cyclization mechanisms considerably decrease in going from lithium to potassium as counterion.

Comparative semiempirical and DFT study of styrylnaphthalenes and styrylquinolines and their photocyclization products

AbstractSemiempirical molecular orbital (PM3, PM6, and RM1) and density functional theory (DFT) (B3LYP/6‐31G*) studies are carried out for 1‐ and 2‐styrylnaphthalenes and their aza‐derivatives—2‐ and 4‐styrylquinolines. Relative stabilities of three isomeric forms: E‐ and Z‐isomers and the closed‐ring dihydrocyclophotoproduct (derivative of dihydrophenanthrene) are calculated. Compared to PM3, PM6 and especially RM1 understate heats of formation; in some cases, PM6 and RM1 even place Z‐isomer in energy below E‐isomer. PM3 rather close to DFT predicts heats of isomerization reaction, whereas PM6 and especially RM1 underestimate these values. Semiempirical methods in comparison with DFT markedly underestimate heats of cyclization reaction; however, reproduce trends in relative stabilities of different isomers in dependence on the structure of styrylnaphthalenes and styrylquinolines. Qualitative correlation is found between calculated relative stabilities of the closed‐ring forms (heats of cyclization reaction) and experimental data: cyclized products with low heats of cyclization are observed in steady‐state photolysis and those with high heats of cyclization are not. In the latter case, the closed‐ring compounds, if formed in the excited state, due to thermal instability decompose rapidly with ring opening in the ground state that prevents their observation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Preferential Encapsulation and Stability of La3N Cluster in 80 Atom Cages: Experimental Synthesis and Computational Investigation of La3N@C79N

We report the synthesis and electronic stabilization of La(3)N@C(79)N. Unsuccessful efforts to encapsulate bulky La(3)N clusters in small C(80) cages have been attributed to large ionic radii. The preferred species for La(3)N clusters in all-carbon cages is La(3)N@C(96). A surprising finding is the synthesis of La(3)N@C(79)N, a new metallofullerene present in higher abundance than La(3)N@C(96). This reduction in cage size from 96 to 80 atoms reflects the significance and role of electronic effects. To understand the geometric and electronic properties of this first metallic nitride azafullerene (M(3)N@C(79)N, M = La), density functional theory (DFT) investigations were performed on a number of isomers. Results indicate a preferred N-substitution at the 665 junction site on the cage in lieu of a 666 substitution. The relative stabilities of different isomers can be well reproduced by using the minimum distance between the metal atom and the nitrogen atom of the cage (R(N'M)(min)). Long R(N'M)(min) values indicate distant contacts between six atoms that bear significantly large positive charges: the three metal atoms and the three carbon atoms bonded with the nitrogen atom in the cage, which are favored. These results suggest a dominant electronic effect on the stabilities of metalloazafullerenes. Interestingly, spin densities of the 665 substitution isomers of La(3)N@C(79)N are located predominantly in the metal cluster, while spin densities of the 666 substitution isomers are primarily on the cage.

New organogermanium cations [RGe(OCH2CH2NME2)2]+ with intramolecular N→Ge coordination bonds

New organohalogermanes RGe(OCH2CH2NMe2)2X (R = Ph, X = I (5); R = Me, X = Cl (6) or I (7)) with an intramolecular N→Ge coordination bond were synthesized. According to the 1H and 13C NMR spectroscopic data, iodides 5 and 7 exist in solution as ionic compounds with the pentacoordinated germanium atom. In solution of compound 4 (R = Ph, X = Cl), there is an equilibrium between the ionic and covalent forms. The equilibrium shifts toward the ionic form with increasing solvent polarity or temperature. In solution, chloride 6 is a covalent compound. The structures and relative stabilities of different isomers of compounds 4–7 were studied by quantum chemical calculations at the density functional level of theory.