Relative Stabilities Of Different Isomers Research Articles

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.

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.

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.

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.

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.

Theoretical study of solvent effects on the structures and isomerization of silylenoid H2SiLiF

The structures and isomerization of silylenoid H2SiLiF are investigated by density functional theory (DFT) at B3LYP/6-311+G(d,p) level. The solvent effects are modeled using the self-consistent reaction field (SCRF) method with Tomasi’s polarized continuum model (PCM). Five representative solvents, i.e. benzene, ether, THF, acetone, and DMSO, are chosen for this work. Special attention is paid to THF solvent. The results indicate that the polarity of solvents has played an important role on the structures and relative stabilities of different isomers. Contrary to the three-membered ring structure 1, the relative stability of the “classical” tetrahedron structure 4 increases with increasing dielectric constants (e) of solvents. The σ-complex isomer 3 is most unstable structure. Although the relative energies are reduced with increasing dielectric constants (e) of solvents, the p-complex structure 2 still has the lowest energy. The effects of solvents on the dipole moments and charge distributions are also discussed.

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of formamide with hydrogen peroxide

For the first time, the hydrogen bonding of 1:1 complexes formed between formamide and hydrogen peroxide molecule have been completely investigated in the present study using density functional theory (DFT), second-order Moller-Plesset Perturbation (MP2) and Hartree-Fock (SCF) method at varied basis set levels from 6-31g to 6-31++g(d,p). Five reasonable geometries on the potential energy hypersurface of formamide and hydrogen peroxide system are considered with the global minimum being a cyclic double-hydrogen bonded structure. The relative stability order of the five structures is FH1>FH2>FH3>FH4≈FH5. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported. Finally the solvent effects on the geometries of the formamide–hydrogen peroxide complexes have also been investigated using self-consistent reaction-field (SCRF) calculations at the B3LYP/6-31++g(d,p) level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. In water, FH2 disappears and the relative stability order changes to FH3>FH1>FH5≈FH4 which is not in consistent with the gas phase one.

Density functional theory study of the hydrogen bonding interaction in formamide dimer

The hydrogen bonding of 1:1 complexes formed between formamide and formamide molecule has been completely investigated in the present study using density functional theory (DFT) method at varied basis set levels from 6-31G to 6-311++G(2d,2p). The large basis sets 6-311++G(d,p) and 6-311++G(2d,2p) have been employed to determine the equilibrium structure and vibrational frequencies of the interacting complexes. Five reasonable geometries on the potential energy hypersurface of formamide dimer system are considered with the global minimum, four of which are cyclic double-hydrogen bonded structure and one is one-hydrogen bonded structure. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported. Finally the solvent effects on the geometries of the formamide dimer have also been investigated using self-consistent reaction-field (SCRF) calculations at the B3LYP/6-311++G** level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers.

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

AbstractThe hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Conformational Analysis of Trans-3, 6-Dibutanal-1, 2, 4, 5-Tetroxane

We report the results of theoretical semiempirical AM1 and PM3 molecular orbital methods on the conformational analysis of the title compound. The relative stability of different isomers and conformers are discussed on the basis of well defined electronic and steric effects, which are rather helpful in order to understand the relative stabilities.

Theoretical study of helical structure caused by chirality of cysteine dimer

In this work we report a theoretical study of the helix structure and chiral discrimination on the interactions between the chiral cysteine–cysteine. Two reasonable geometries on the potential energy hypersurface of the cysteine–cysteine system are considered with the global minimum. Accurate geometric structures, relative stabilities, harmonic vibrational frequencies, and infrared (IR) intensities were investigated. To take into account the water solvation effect, the Onsager model within the self-consistent reaction field (SCRF) method and the polarized continuum (PCM) method were used to evaluate the interaction energy, ΔGsolv at the same level employed in the gas phase. The results indicate that the polarity of the solvent plays an important role in the structures and relative stabilities of different isomers. Computational results indicate that the global minimum should be conformer I regardless of whether in the gas phase or in aqueous solution, which differs from previous theoretical reports. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Theoretical study of chiral discrimination in the hydrogen bonding complexes of the hydrazine dimer

AbstractIn this work, the discrimination of different chiral forms of the hydrazine dimer were investigated using Density Functional Theory (DFT) and second‐order Moller–Plesset Perturbation (MP2) theory at basis set levels from 6‐31g to 6‐31++g(d,p). Four chiral structures were studied. The optimized geometric parameters, interaction energies, and chirodiastatic energy for various isomers at different levels were estimated. Finally, the solvent effects on the geometries of the hydrazine dimers were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐31++g(d,p) level. The results indicate that the polarity of the solvent has played an important role in the structures and relative stabilities of different isomers. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Density Functional Theory Study of the Hydrogen-Bonding Interaction of 1:1 Complexes of Alanine with Water

The hydrogen bonding of 1:1 complexes formed between alanine and water molecules has been completely investigated in the present study using density functional theory, method B3LYP at varied basis set levels from 6-31G to 6-311++G(d,p) and the second-order Møller−Plesset perturbation method at the 6-31++G(d,p) level. Eight reasonable geometries on the potential energy hypersurface of the alanine and water system are considered with the global minimum. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The infrared spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the alanine−water complexes have also been investigated using self-consistent reaction-field calculations at the B3LYP/6-311++G(d,p) level. The results indicate that the polarity of the solvent plays an important role in determining the structures and relative stabilities of different isomers.