Structure, stability and dissociation of silanitriles RSiN (R = H2B, H2N, H2P)

Structure, stability, and dissociation of H₂BSiN, H₂NSiN, H₂PSiN and their isomers H₂BNSi, H₂NNSi, H₂PNSi have been studied in detail using ab initio MP2 and CCSD(T) methods. After dissociation of H₂BNSi, H₂NNSi, H₂PNSi and their isomers, the fragmented atoms have been considered to be either in their ground state or in their valence excited state in various dissociation channels. Only allowed dissociations of these molecules are considered. Various dissociation channels of H₂BNSi, H₂NNSi, H₂PNSi and their isomers have been explored and interesting trends are observed for the dissociation of stable isomers H₂BNSi, H₂NNSi, H₂PNSi and less stable isomers H₂BSiN, H₂NSiN, H₂PSiN. The effect of substituents on their structural properties has been discussed. The potential energy surfaces for the RSiN ? RNSi isomerization reactions have been analyzed. The structural properties of these molecules agree well with the theoretical values wherever available.     

Molecular fragmentations: Part IX. Structures and energies of mass spectral fragments derived from xanthan hydride, 5-amino-1,2,4-dithiazolin-3-thione

Structures and energies have been calculated, in the MNDO approximation, for xanthan hydride (C₂H₂N₂S₃) and its molecular cation, and for the mass spectral fragment ions H₂NCNCS⁺, HNCNCS⁺, CS₂⁺, H₂N₂CS⁺ (two isomers), HN₂CS⁺, S₂⁺, H₂NCS⁺ (three isomers), HNCS⁺ (two isomers), H₃N₂C₂⁺ (four isomers), CS⁺ and HNCS⁺² (two isomers), together with the corresponding neutral fragments.     

Theoretical study of 2,5-diphenyl-1,4-distyrylbenzene (A model compound of PPV): A comparison of the electronic structure and photophysical properties of cis- and trans-isomers

2,5-Diphenyl-1,4-distyrylbenzene (DPDSB), a model compound of PPV, have been synthesized with two isomers: cis- and trans-DPDSB in our lab. We have found three distinguishing features of photophysical properties between these two isomers. To explain these three special spectral behaviors, the quantum-chemical computations were performed to investigate the ground-state and excited-state molecular geometries, electronic structure, absorption and emission properties, potential–energy curve of the ground-state and excited-state, and so on. According to our calculated results, the nature causing above distinguishing photophysical properties is larger configuration displacement of cis-DPDSB than trans-DPDSB from the ground-state to the excited-state, especially for the changes in torsion angle along vinyl double bonds in cis-DPDSB.     

Structures and electronic properties of the small rubidium‐doped silicon RbSin (n = 1–12) clusters

The geometries, relative stabilities, and electronic properties of small rubidium‐doped silicon clusters RbSi_n (n = 1–12) have been systematically investigated using the density functional theory at the B3LYP/GENECP level. The optimized structures show that lowest‐energy isomers of RbSi_n are similar with the ground state isomers of pure Si_n clusters and prefer the three‐dimensional for n = 3–12. The relative stabilities of RbSi_n clusters have been analyzed on the averaged binding energy, fragmentation energy, second‐order energy difference, and highest occupied molecular orbital‐lowest unoccupied molecular orbital energy gap. The calculated results indicate that the doping of Rb atom enhances the chemical activity of Si_n frame and the magic number is RbSi₂. The Mulliken population analysis reveals that the charges in the corresponding RbSi_n clusters transfer from the Rb atom to Si atoms. The partial density of states and chemical hardness are also discussed. © 2014 Wiley Periodicals, Inc.     

Molecular Properties of Additive Poly(bis(trimethylsilyl)tricyclonones) with Vicinal and Geminal Side Substituents

The molecular properties of the additive poly(bis(trimethylsilyl)tricyclononene) with the vicinal position of two side groups Si(CH₃)₃ in the monomer unit are studied for the first time, and its conformational and kinetic properties are compared with those of the isomer with the geminal position of the same groups. Using the methods of static/dynamic light scattering and viscometry for the samples of the vicinal isomer, the hydrodynamic parameters of molecules are determined and their molecular mass dependences in toluene are ascertained. In addition, the Kuhn segment length of this isomer is estimated. The kinetic rigidity of vicinal and geminal isomers is evaluated by ¹H NMR relaxation from the mobility of protons in Si(CH₃)₃ groups. The reasons behind different gas permeabilities of the films based on the polymers with the vicinal and geminal positions of Si(CH3)3 side groups in the monomer unit are discussed.     

Stabilizing the Exotic Carbonic Acid by Bisulfate Ion

Carbonic acid is an important species in a variety of fields and has long been regarded to be non-existing in isolated state, as it is thermodynamically favorable to decompose into water and carbon dioxide. In this work, we systematically studied a novel ionic complex [H₂CO₃·HSO₄]⁻ using density functional theory calculations, molecular dynamics simulations, and topological analysis to investigate if the exotic H₂CO₃ molecule could be stabilized by bisulfate ion, which is a ubiquitous ion in various environments. We found that bisulfate ion could efficiently stabilize all the three conformers of H₂CO₃ and reduce the energy differences of isomers with H₂CO₃ in three different conformations compared to the isolated H₂CO₃ molecule. Calculated isomerization pathways and ab initio molecular dynamics simulations suggest that all the optimized isomers of the complex have good thermal stability and could exist at finite temperatures. We also explored the hydrogen bonding properties in this interesting complex and simulated their harmonic infrared spectra to aid future infrared spectroscopic experiments. This work could be potentially important to understand the fate of carbonic acid in certain complex environments, such as in environments where both sulfuric acid (or rather bisulfate ion) and carbonic acid (or rather carbonic dioxide and water) exist.     

Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MS

Ion mobility-mass spectrometry (IMS-MS) and molecular modeling techniques have been used to characterize ovalbumin N-linked glycans. Some glycans from this glycoprotein exist as multiple isomeric forms. The gas-phase separation makes it possible to resolve some isomers before MS analysis. Comparisons of experimental cross sections for selected glycan isomers with values that are calculated for iterative structures generated by molecular modeling techniques allow the assignment of sharp features to specific isomers. We focus here on an example glycan set, each having a m/z value of 1046.52 with formula [H₅N₄+2Na]²⁺, where H corresponds to a hexose, and N to a N-acetylglucosamine. This glycan appears to exist as three different isomeric forms that are assignable based on comparisons of measured and calculated cross sections. We estimate the relative ratios of the abundances of the three isomers to be in the range of ∼1.0:1.35:0.85 to ∼1.0:1.5:0.80. In total, IMS-MS analysis of ovalbumin N-linked glycans provides evidence for 19 different glycan structures corresponding to high-mannose and hybrid type carbohydrates with a total of 42 distinct features related to isomers and/or conformers.     

Theoretical study of two C50H40 isomers with three dodecahedrane cages sharing two pentagons

Structures, energies, and vibrational frequencies have been calculated for two C₅₀H₄₀ isomers with three dodecahedrane cages sharing two pentagons at the B3LYP/6‐31G* level of theory. Thus, two C₅₀H₄₀ isomers have the form of coplanar tri‐dodecahedrane‐cage molecules. The symmetry of one isomer is D_5d and that of another is C_2V. Heats of formation and vertical ionization energies for two C₅₀H₄₀ isomers have been estimated in this study. Heats of formation as well as vibrational analysis indicate that two C₅₀H₄₀ isomers enjoy sufficient stability to allow for its experimental preparation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of isomerism of compounds of N2 and N2H2 molecules with aluminum clusters Al13 and Al12Ti

Segments of the potential energy surfaces corresponding to successive elementary stages of multistep fragmentation of nitrogen and diimine molecules upon their reaction with the aluminum cluster Al₁₃ and its doped analogue Al₁₂Ti have been calculated by the density functional theory method. The minimum energy pathways of these reactions have been calculated for the stages of physisorption, chemisorption, and N₂ and N₂H₂ fragmentation with different ways of insertion of fragments into the Al₁₃ and Al₁₂Ti cages. Relative energies, structural characteristics, and vibrational frequencies of coordinated and fragment isomers have been calculated, the barriers separating these isomers have been evaluated, and molecular diagrams of the reactions have been constructed. The effect of doping on the relative energies of intermediates and activation barriers has been considered. A conclusion has been drawn that doping with titanium should facilitate the reactions of molecular nitrogen with aluminum clusters. Unusual isomers with a five- and six-coordinate nitrogen atom N* have been localized. The results are compared with the data of analogous previous calculations of the PES of isomers corresponding to stepwise fragmentation of an acetylene molecule in related Al₁₃C₂H₂ and Al₁₂TiC₂H₂ derivatives.     

Theoretical study of Pu and Am tetracarbide molecules

The electronic structure and ground‐state molecular properties of Pu and Am tetracarbides have been investigated by relativistic multireference calculations using CASSCF/CASPT2 theory as well as by density functional theory in conjunction with relativistic pseudopotentials. The CASSCF/CASPT2 treatment has been extended by spin–orbit coupling effects for selected species using the CAS state‐interaction method. The five atoms can form various structural isomers, from which 12 ones have been identified in our study. The electronic ground state in both molecules corresponds to a planar fan‐type structure of C_2v symmetry, in which the actinide atom is connected to a bent C₄ moiety. The other structures are much higher in energy, the ones computed in this study appear between 250 and 1050 kJ/mol. The bonding characteristics in the most relevant structures have been analyzed on the basis of the valence molecular orbitals and natural bond orbital analysis. The most stable structures have been characterized by their spectroscopic (vibrational and electron) properties. © 2014 Wiley Periodicals, Inc.     

A molecular orbital study of the electronic structure and stereochemistry of dithiocyanate diamine and dicyanate diamine cupric complexes

CNDO/2—UHF molecular orbital calculations have been performed with the aim of studying the electronic structure and stereochemistry of the complexes Cu(NH₃)₂(NCX)₂ (X = O, S). Orbital energies, atomic charges, Wiberg indices, spin densities, total molecular energies and their partitioning into metal—ligand and ligand—ligand interactions have been calculated for three model structures of each complex. The role of axial interactions in stabilizing the planar arrangement of theCuN₄ chromophore is discussed. The harmonic force constants of some deformation vibrations of coordinated NCX groups have been estimated for the trans isomers and these estimates are compared with the values for the free ligands.     

A quantum chemical study of three isomers of N20

Ab initio molecular orbital (MP2) and density functional theory (B3LYP) calculations using different basis sets have been employed to study the structures, energetics and vibrational frequencies of the large homonuclear polynitrogen compound, N₂₀. In the present study, three distinct forms were found to represent local minima on the potential energy surface. They are the fullerene-type cage form of I_h symmetry, a corannulene-like bowl form of C_5v symmetry, and a ring isomer with D₅ symmetry of which the cage form turns out to be the highest energy form. Both the bowl and ring forms are calculated to be more stable than the cage form by about 200 kcal/mol. The molecular properties calculated for these isomers may serve as valuable predictions for future experimental searches for new high energy density materials (HEDM).     

Microwave spectrum,structure, dipole moment and internal rotation of ethyl fluorosilane

Microwave spectra of the trans and gauche isomers of ethyl fluorosilane and their eleven isotopically substituted species have been measured. The r_s structures of the two isomers were determined from the observed moments of inertia. The molecular structures found for the two isomers in the present study are compared with those of analogous molecules. Dipole moments of the two isomers were determined by Stark-effect measurements and are also compared with those of analogous molecules. The energy difference between the trans and gauche isomers was obtained from the relative intensity measurements of the spectra and the barrier to internal rotation of the methyl group for the gauche isomer was obtained from the A—E splittings of the spectra in the first excited methyl torsional state. The V₃ value was 2775 ± 25 cal mol^?1.     

A non-empirical molecular orbital study of valence tautomers of C2H3N

The valence tautomers of C₂H₃N have been examined by non-empirical molecular orbital calculations using two split-valence shell basis sets. All geometries were fully optimized using the 4–31G basis set and these structures were then used in 6–31G basis set calculations. The order of stability of the three possible cyclic isomers is 1-azirine > cyclic carbene > 2-azirine. The profiles for conversion of vinylmethylene into cyclopropene, vinylnitrene into 1-arizine, and iminomethylene into 2-azirine have all been shown to have barriers.     

The COMPASS force field: parameterization and validation for phosphazenes

A new, condensed-phase optimised ab-initio force field, COMPASS, has been developed recently. In this paper, the validation of COMPASS for phosphazenes is presented. The functional forms of this force field are of the consistent force field (CFF) type. Charges and bonded terms were derived from HF/6–31G1 calculations, while the nonbonded parameters (L-J 9-6 vdW potential) were initially transferred from the polymer consistent force field, pcff, and optimised using MD simulations of condensed-phase properties. As a validation of COMPASS, molecular mechanics calculations and molecular dynamics simulations have been made on a number of isolated molecules, liquids, and crystals. The calculated molecular structure, vibration frequencies, conformational properties for isolated molecules, crystal cell parameters and density, liquid density, and heat of evaporation agreed favourably with most experimental data. The special conformational properties of the tetracyclophosphazenes, (NPCI₂)₄ and (NPF₂)₄, in the solid state are discussed based on molecular mechanics and CASTEP ab-initio calculations. The effect of nonbonded cutoff distance and different algorithms for pressure control in NPT simulation was also investigated. Finally, molecular dynamics using the COMPASS force field was used to predict properties of three isomers of high-molecular-weight amorphous poly(dibutoxyphosphazenes). In this case, excellent agreement was achieved between densities and glass transition temperatures obtained from dynamics and experimental data.     

Gas phase bimolecular chemistry of isomeric C3H6Br+ cations

The gas phase chemistry of C₃H₆Br⁺ cations generated via low energy electron impact on various dibromopropanes has been studied by using Fourier transform ion cyclotron resonance mass spectrometry. Neutral substrate molecules that have been selected to probe the bimolecular reactivity of the C₃H₆Br⁺ isomers are ammonia, methylamine, trimethylamine, cis-butene, and 2, 3-dimethyl-2-butene. At least three different isomers are characterized on the basis of their different reactivity toward the various substrate molecules. It is suggested that these isomers have (a) the 2-bromo-2-propyl cation structure, (b) the propylenebromomum ion structure, and (c) the cyclic four-membered trimethylenebromonium ion structure. The 2-bromo-2-propyl cations react predominantely via proton transfer. This reaction is hampered for the propylenebromonium ions, which react mainly as electrophiles or bromanyl cation donors. Cyclic trimethylenebromoruum ions react predominantly via adduct formation, even under low pressure conditions, which implies that tturd body collisions are not the only stabilization mechanism.     

C3H4: Theoretical study of structures and stabilities of isomers

The various isomers including stable structures, carbenes, and diradicals on the C₃H₄ surface have been investigated. The two carbenes propenylidene and cyclopropylidene have been found to have singlet ground states. Vinylmethylene is predicted to have a triplet ground state with a planar diradical type of structure. The syn and anti forms of this state are degenerate. This is in agreement with the observation of two triplet states in the electron spin resonance (ESR ) spectra. The π electrons are found to be delocalized over the three carbons. The singlet diradical structures are found to be more stable than the carbene structures, which retain the CH₂ (DOUBLE BOND) CH allylic structures. The orbital compositions of the frontier orbitals of all systems have been determined to examine the nature of these orbitals. © 1996 John Wiley & Sons, Inc.     

Computational studies on C24H8, C28H12, and C32H16 isomers in which the cubane,pentaprismane, or hexaprismane cages are linked by four CC bonds

Quantum-chemical calculations on C₂₄H₈, C₂₈H₁₂, and C₃₂H₁₆ isomers in which the cubane, pentaprismane, or hexaprismane cages are linked by four CC bonds have been performed using density functional theory (DFT) method. The geometric structures, energies, vibrational frequencies, and vertical ionization energy as well as vertical electron affinity of various isomers have been obtained at the B3LYP/6-31G7 level of theory. Meanwhile, the present paper has also computed the enthalpies of formation for different isomers so as to evaluate their stability from a thermodynamic point of view. There exists two different isomers for C₂₈H₁₂ and C₃₂H₁₆ in which the prismane (pentaprismane or hexaprismane) cages are parallel or perpendicular to each other. It has been concluded that the isomer in which the prismane (pentaprismane or hexaprismane) cages are perpendicular is more stable and has relatively smaller heat of formation.     

An Alternate [2×2] Grid Constructed Around TiO4N2 Units

The formation of a tetranuclear self-assembled species constructed around a TiO₄N₂ motif is reported. This aggregate is generated from Ti(OⁱPr)₄, 2,2’-bipyrimidine (bpym) and a bis-biphenol strand (L²H₄) where two 2,2’-biphenol units are connected with a biphenyl spacer. The solid-state structure of the [Ti₄(L²)₄(bpym)₄] architecture reveals the formation of an unprecedented chiral alternate [2×2] grid. In addition to the structural characterization of the [Ti₄(L²)₄(bpym)₄] architecture, geometry optimisation on various possible isomeric tetrameric assemblies ([2×2] grid, alternate [2×2] grid, circular helicate or cyclic hemihelicate) is performed using DFT calculations. These results confirm the higher stability of the alternate [2×2] grid over the other possible tetranuclear isomers and allow examining the replacement of the bpym ligands by two novel diimine chelates within the tetranuclear assembly (2,2’-bipyridine=bipy and 2,2’-bipyrazine=bipyraz). From this initial theoretical investigation, the competition between these three nitrogen ligands in the course of the self-assembly process is next evaluated. Overall, this investigation shows that the exclusive formation of the alternate [2×2] grid is driven by CH⋅⋅⋅N interactions.     

Aromatic N-Heterocyclic superalkali M@C4H4N2 complexes (M=Li,Na, K); A promising potential hydrogen storage system

In search of a potential hydrogen storage material, we have used three different aromatic N-heterocyclic systems; Pyrazine, Pyrimidine, and Pyridazine. The alkali (Li, Na, and K) metallated heterocyclic systems (M@C₄H₄N₂) are stabilized as cation found to be superalkali with a vertical electron affinity ranges from 4.42 to 3.97 ​eV. First principle calculations reveal that M@heterocylclic systems can adsorb up to 10–18H₂ molecules with gravimetric wt% of 17. It has been observed that all the trapping process belongs to physisorption as H₂ are almost in a molecular form with a slight increase in bond length. Binding energy values favor gradual H₂ adsorbtion. Superalkali nature is gradually increasing upon the increasing number of H₂ molecules but attains a constant value after certain numbers. Among three isomers Pyrazine, Pyrimidine, and Pyridazine, Li@Pyrazine complex is found to be the most suitable for H₂ storage.