Relativistic effects on inversion barriers of pyramidal group 15 hydrides

Quantum chemistry is an important tool for determining general molecular properties, although relativistic corrections are usually required for systems containing heavy and super heavy elements. Non‐relativistic along with relativistic two‐ and four‐component electronic structure calculations done with the CCSD‐T method and the new RPF‐4Z basis set have therefore been applied for determining inversion barriers, corresponding to the change from a pyramidal (C_3v) ground‐state structure to the trigonal planar (D_3h) transition state, TS, of group 15 hydrides, XH₃ (X= N, P, As, Sb, and Bi). The ground‐state structure of the McH₃ molecule, which contains the super heavy element Moscovium, is also predicted as pyramidal (C_3v), with an atomization energy of 90.8 kcal mol⁻¹. However, although non‐relativistic calculations still provided a D_3h planar TS for McH₃, four‐component relativistic calculations based on single‐reference wave functions are unable to elucidate the definitive TS geometry in this case. Hence, the results show that relativistic effects are crucial for this barrier determination in those hydrides containing Bi and Mc. Moreover, while the scalar relativistic effects predominate, increasing barrier heights by as much as 17.6 kcal mol⁻¹ (32%) in BiH₃, the spin‐orbit coupling cannot be disregarded in those hydrides containing the heaviest group 15 elements, decreasing the barrier by 2.5 kcal mol⁻¹ (4.5%) in this same molecule.     

Theoretical study of the C3Cl radical and its cation

A theoretical study of C₃Cl and C₃Cl⁺ isomers has been carried out. The global minimum for C₃Cl is a cyclic C_2V species (a three-membered ring with an exocyclic chlorine atom). However, a quasi-linear CCCCl structure is predicted to lie only 3-5 kcal mol⁻¹ higher. This quasi-linear structure is floppy, since the linear arrangement lies only 2-3 kcal mol⁻¹ higher in energy. The cyclic and open-chain isomers have dipole moments of 1.986 and 3.363 D, respectively. In C₃Cl⁺ the global minimum is a linear singlet species, the singlet cyclic isomer lying about 19 kcal mol⁻¹ higher. The ionization potentials of cyclic and open-chain C₃Cl are estimated to be 9.17 and 8.21 eV, respectively, suggesting that these species should be easily ionized if present in the interstellar medium.     

The thermodynamic stability of P8, A CBS‐Q study

The thermodynamic stabilities of P₂, P₄, and three P₈ cage structure were investigated through high‐precision CBS‐Q calculations. The CBS‐Q values for the bond energy of P₂ (ΔE_o: +115.7 kcal mol⁻¹) and the formation of P₄ from P₂ (Δ E_o:‐56.6 kcal mol⁻¹) were in excellent agreement with the experimental values (E_o: +117 and ‐56.4 kcal mol⁻¹ respectively). Among the P₈ cages, the cubane structure was the least stable (Δ E_o +37 kcal vs. 2×P₄). The most stable P₈ isomer adopts a cuneane structure resembling S₄N₄, and is more stable than white phosphorus at T = 0 K (Δ E_o −3.3 kcal mol⁻¹), but still unstable under standard conditions for entropic reasons (Δ G^o of +8.1 kcal mol⁻¹ vs. 2×P₄). The CBS‐Q energies represent significant revisions (6–20 kcal mol⁻¹) of previous computational predictions obtained by high‐level single method calculations. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:453–457, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20119     

Infrared,Raman and NMR spectra,conformational stability,and ab initio calculations of divinylmethoxyborane

The infrared spectra (4000–50 cm⁻¹) of gaseous and solid divinylmethoxyborane, (CH₂=CH)₂BOCH₃, as well as the Raman spectra (3500–20 cm⁻¹) of the liquid and solid have been recorded. Qualitative depolarization values have been obtained from the Raman spectrum of the liquid. All normal modes, except the torsions, have been assigned based on infrared band contours, depolarization values, group frequencies, and normal coordinate calculations. From a comparison of the spectra in the fluid and solid states, it is concluded that the molecule exists predominantly in a single conformation in all physical states. Frequencies and potential energy distributions for the normal modes have been calculated with the 3–21G basis set. A comparison of these calculated frequencies to the observed spectra is consistent with the predominant form having a “planar” heavy atom skeleton with C_s, symmetry. From the variable low temperature ¹³C NMR data, a barrier to rotation about the B-O bond of 10.1 ± 0.1 kcal mol⁻¹ has been determined, which is in excellent agreement with a barrier of 8.5 kcal mol"1 obtained from ab initio calculations. Structural parameters, conformational stability, and barriers to internal rotation have been obtained from ab initio Hartree-Fock gradient calculations employing both the 3–21G and 6–31G^* basis sets. The results are compared to the corresponding data for some similar organoboranes.     

Mechanism of nucleophilic fluorination promoted by bis‐tert‐alcohol‐functionalized crown‐6‐calix[4]arene

Theoretical calculations were performed to elucidate the ability of the recently reported bis‐tert‐alcohol‐functionalized crown‐6‐calix[4]arene (BACCA) molecule to promote nucleophilic fluorination of alkyl mesylates with cesium fluoride reagent. It was found that a similar structure, named BACCAt, can separate the cesium fluoride ion pair in tert‐butanol solution. This separation has a free energy cost, even considering the double hydrogen bonds with the fluoride ion. The solvent has an important effect on the stabilization of this complex, due to interaction with the high dipole moment of the separated ion pair. The observed rate acceleration effect involves a structure with double hydrogen bonds between the BACCAt and the centers of negative charges of the S_N2 transition state. The predicted free energy barrier of 27.3 kcal mol⁻¹ is in excellent agreement with the estimated experimental value of 26.2 kcal mol⁻¹.     

On the Stability of Interactions between Pairs of Anions – Complexes of MCl3− (M=Be,Mg, Ca,Sr, Ba) with Pyridine and CN−

The ability of the central M atom of the MCl₃⁻ anion, with M=Be, Mg, Ca, Sr, Ba, to engage in a noncovalent bond with an approaching nucleophile is gauged by ab initio methods. The N atom of pyridine forms a M⋅⋅⋅N bond with an interaction energy between 12 and 21 kcal mol⁻¹, even though the π-hole above the M atom is not necessarily positive in sign. Despite a strong Coulombic repulsion between two anions, CN⁻ is also able to approach the M atom so as to engage in a metastable complex that is higher in energy than the individual anions. The energy barrier separating this complex from its constituent anion pair is roughly 20 kcal mol⁻¹. Despite the endothermic formation reaction energy of the CN⁻⋅⋅⋅MCl₃⁻ complex, the electron topology signals a strong interaction, more so than in pyridine⋅⋅⋅MCl₃⁻ with its exothermic binding energy. The dianionic complex is held together largely on the strength of interorbital interactions, thereby overcoming a repulsive electrostatic component. The latter is partially alleviated by the pyramidalization of the MCl₃ unit which makes its π-hole more positive. The complex sinks below the separate monomers in energy when the system is immersed in an aqueous medium, with a binding energy that varies from as much as 20 kcal mol⁻¹ for Be down to 1.2 kcal mol⁻¹ for Ba.     

London Dispersion Effects in a Distannene/Tristannane Equilibrium: Energies of their Interconversion and the Suppression of the Monomeric Stannylene Intermediate

Reaction of {LiC₆H₂−2,4,6-Cyp₃⋅Et₂O}₂ (Cyp=cyclopentyl) ( 1 ) of the new dispersion energy donor (DED) ligand, 2,4,6-triscyclopentylphenyl with SnCl₂ afforded a mixture of the distannene {Sn(C₆H₂−2,4,6-Cyp₃)₂}₂ ( 2 ), and the cyclotristannane {Sn(C₆H₂−2,4,6-Cyp₃)₂}₃ ( 3 ). 2 is favored in solution at higher temperature (345 K or above) whereas 3 is preferred near 298 K. Van't Hoff analysis revealed the 3 to 2 conversion has a ΔH=33.36 kcal mol⁻¹ and ΔS=0.102 kcal mol⁻¹ K⁻¹, which gives a ΔG^{300 K}=+2.86 kcal mol⁻¹, showing that the conversion of 3 to 2 is an endergonic process. Computational studies show that DED stabilization in 3 is −28.5 kcal mol⁻¹ per {Sn(C₆H₂−2,4,6-Cyp₃)₂ unit, which exceeds the DED energy in 2 of −16.3 kcal mol⁻¹ per unit. The data clearly show that dispersion interactions are the main arbiter of the 3 to 2 equilibrium. Both 2 and 3 possess large dispersion stabilization energies which suppress monomer dissociation (supported by EDA results).     

Silaacetylene: A possible target for experimental studies

The equilibrium geometries and transition states for interconversion of the CSiH₂ isomers in the singlet electronic ground state are optimized at the MP2 and CCSD(T) levels of theory using a TZ2P basis set. The heats of formation, vibrational frequencies, infrared intensities, and rotational constants are also predicted. There are three energy minima on the CSiH₂ potential energy surface. Energy calculations at CCSD(T)/TZ2P(fd) + ZPE predict that the global energy minimum is silavinylidene (1), which is 34.1 kcal mol⁻¹ lower in energy than trans-bent silaacetylene (2) and 84.1 kcal mol⁻¹ more stable than the vinylidene isomer (3). The barrier for rearrangement 2→1 is calculated at the same level of theory to be 5.1 kcal mol⁻¹, while for the rearrangement 3→2 a barrier of 2.7 kcal mol⁻¹ is predicted. The natural bond orbital (NBO) population scheme indicates a clear polarization of the C(SINGLE BOND)Si bonds toward the carbon end. A significant ionic contribution to the C(SINGLE BOND)Si bonds of 1 and 2 is suggested by the NBO analysis. The C(SINGLE BOND)Si bond length of trans-bent silaacetylene (2) is longer than previously calculated [1.665 Å at CCSD(T)/TZ2P)]. The calculated carbon-silicon bond length of 2 is in the middle between the C(SINGLE BOND)Si double bond length of 1 (1.721 Å) and the C(SINGLE BOND)Si triple bond of the linear form HCSiH (4), which is 1.604 Å. Structure 4 is a higher-order saddle point on the potential energy surface. © 1996 by John Wiley & Sons, Inc.     

Reactions of Au+ and Au− with benzene and fluorine-substituted benzenes

Reactions of gold anions and cations generated by laser desorption/ionization were studied in the FTICR spectrometer. Au⁻ associated with C₆F₆ to give the novel Au⁻(C₆F₆) complex, whose binding energy was estimated to be 24 ± 4 kcal mol⁻¹ from analysis of the radiative association (RA) kinetics. Au⁺ associated with C₆F₅H to give Au⁺(C₆F₅H), with binding energy estimated to be 31 kcal mol⁻¹. Au⁺ reacted with C₆H₆ to form the well known Au⁺(C₆H₆) and Au⁺(C₆H₆)₂ complexes. The observation of rapid charge transfer from Au⁺(C₆H₆) to C₆H₆ was interpreted as showing that benzene binds more strongly to neutral Au than to Au⁺. The neutral Au–C₆H₆ bond is accordingly concluded to be stronger than about 70 kcal mol⁻¹.     

Structure and conformational processes of bis(o-cumyl)sulfide, sulfoxide and sulfone

The NMR solution spectra of the title sulfide and sulfone show decoalescence of the geminal methyl signals of the isopropyl groups at low temperature (−178 °C for the ¹³C signal of sulfide at 150.8 MHz and −147 °C for the ¹H signal of sulfone at 600 MHz). The barriers for the related dynamic processes were measured (4.3 and 7.0 kcal mol⁻¹ for the sulfide and sulfone, respectively). The preferred conformer of sulfide has a propeller shape with a C₁ symmetry, as suggested by Molecular Mechanics (MM) calculations. In the case of sulfone the preferred conformer has a propeller shape with a C₂-anti symmetry, as indicated by calculations and supported by X-ray crystallographic determination. The computed contour map of the potential energy shows that in both cases the dynamic processes take place via correlated rotations (cogwheel mechanism) of the two aromatic substituents about the Ar-S bonds. Dynamic processes could not be observed by NMR in the title sulfoxide, which was also found to adopt a propeller shaped conformation, as indicated by MM calculations and X-ray diffraction.     

Spin-projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B−DNA by Singlet Oxygen

Guanine is the most susceptible base to oxidation damage induced by reactive oxygen species including singlet oxygen (¹O₂, ¹Δ_g). We clarify whether the first step of guanine oxidation in B−DNA proceeds via either a zwitterionic or a diradical intermediate. The free energy profiles are calculated by means of a combined quantum mechanical and molecular mechanical (QM/MM) method coupled with the adaptive biasing force (ABF) method. To describe the open-shell electronic structure of ¹O₂ correctly, the broken-symmetry spin-unrestricted density functional theory (BS−UDFT) with an approximate spin projection (AP) correction is applied to the QM region. We find that the effect of spin contamination on the activation and reaction free energies is up to ∼8 kcal mol⁻¹, which is too large to be neglected. The QM(AP−ULC−BLYP)/MM-based free energy calculations also reveal that the reaction proceeds through a diradical transition state, followed by a conversion to a zwitterionic intermediate. Our computed activation energy of 5.2 kcal mol⁻¹ matches experimentally observed range (0∼6 kcal mol⁻¹).     

Far-IR spectrum,conformation stability,barriers to internal rotation,vibrational assignment,and ab initio calculations of 3-chloro-2-methylpropene

The far-IR spectrum from 375 to 30 cm⁻¹ of gaseous 3-chloro-2-methylpropene, CH₂=C(CH₃)CH₂Cl, has been recorded at a resolution of 0.10 cm⁻¹. The fundamental asymmetric torsional mode for the gauche conformer is observed at 84.3 cm⁻¹ with three excited states falling to lower frequency. For the higher energy s-cis conformer, where the chlorine atom eclipses the double bond, the asymmetric torsion is observed at 81.3 cm⁻¹ with two excited states falling to lower frequency. Utilizing the s-cis and gauche torsional frequencies, the gauche dihedral angle and the enthalpy difference between conformers, the potential function governing the interconversion of the rotamers has been calculated. The determined potential function coefficients are (in reciprocal centimeters): V₁=189±12, V₂=−358±11, V₃=886±2 and V₄=−12±2 with an enthalpy difference between the more stable gauche and s-cis conformers of 150 ±25 cm⁻¹ (430 ± 71 cal mol⁻¹). This function gives values of 661 cm⁻¹ (1.89 kcal mol⁻¹), 1226 cm⁻¹ (3.51 kcal mol⁻¹) and 812 cm⁻¹ (2.32 kcal mol⁻¹), for the s-cis to gauche, gauche to gauche, and gauche to s-cis barriers, respectively. From the methyl torsional frequency of 170 cm⁻¹ for the gauche conformer, the threefold barrier of 678 cm⁻¹ (1.94 kcal mol⁻¹) has been calculated. The asymmetric potential function, conformational energy difference and optimized geometries of both conformers have also been obtained from ab initio calculations with both the 3–21G^* and 6–31G^* basis sets. A normal-coordinate analysis has also been performed with a force field determined from the 3–21G^* basis set. These data are compared with the corresponding data for some similar molecules.     

A Thermally Populated,Perpendicularly Twisted Alkene Triplet Diradical

Variable‐temperature NMR and ESR spectroscopic studies reveal that bis(dibenzo[a,i]fluorenylidene) 1 possesses a singlet ground state, 1 (S₀), while the 90° twisted triplet 1 (T₁) is populated to a small extent already at room temperature. Analysis of the increasing amount of paramagnetic 1 (T₁) at temperatures between 300 and 500 K yields the exchange interaction J_ex/h c=3351 cm⁻¹ and a singlet–triplet energy splitting of 9.6 kcal mol⁻¹, which is in excellent agreement with calculations (9.3 kcal mol⁻¹ at the UKS BP86/B3LYP/revPBE level of theory). In contrast, the zero‐field splitting parameter D is very small (calculated value −0.018 cm⁻¹) and unmeasurable.     

How different is pyrimidine as a core component of DNA base from its diazine isomers: A DFT study?

Recent photoemission spectroscopic (X‐ray photoemission spectra) study revealed less dramatic chemical changes for pyrimidine (PyM, 1, 3‐diazine) with in its ionization potential. Present systematic study using density functional theory calculations shows that PyM is indeed quite different from its diazine isomers (PyD, 1, 2‐diazine and PyA, 1, 4‐diazine). It is discovered that the most stable isomer PyM is relaxed from C_2V to C₁ point symmetry with a total electronic energy deduction of ?15.86 kcal.mol^?1. Although not substantial, PyM has the smallest molecule shape (electronic spatial extent) and the largest HOMO‐LUMO energy gap of 5.65 eV; only one absorption band in the region of 200–300 nm of the UV‐Vis spectrum but three clusters of chemical shift in the carbon and hydrogen NMR spectra. The energy decomposition analyses revealed that the interaction energy (ΔE_Int) of PyM is preferred over PyA by 4.08 kcal.mol^?1 and over PyD by 22.32 kcal.mol^?1, with the preferred N? C? N bond revealed by graph theory.     

Short intermolecular N—Br...O=C contacts in 1,3‐dibromo‐5,5‐dimethylimidazolidine‐2,4‐dione

In the title compound, C₅H₆Br₂N₂O₂, all atoms except for the methyl group lie on a mirror plane in the space group Pnma (No. 62). All bond lengths are normal and the five‐membered ring is planar by symmetry. Two short intermolecular N—Br...O=C contacts [Br...O = 2.787 (2) and 2.8431 (19) Å] are present, originating primarily from the O‐atom lone pairs donating electron density to the antibonding orbitals of the N—Br bonds (delocalization energy transfers 3.27 and 2.11 kcal mol⁻¹). The total stabilization energies of the Br...O interactions are 3.4828 and 2.3504 kcal mol⁻¹.     

Understanding the Deactivation Pathways of Iridium(III) Pyridine-Carboxiamide Catalysts for Formic Acid Dehydrogenation

The degradation pathways of highly active [Cp*Ir(κ²-N,N-R-pica)Cl] catalysts (pica=picolinamidate; 1 R=H, 2 R=Me) for formic acid (FA) dehydrogenation were investigated by NMR spectroscopy and DFT calculations. Under acidic conditions (1 equiv. of HNO₃), 2 undergoes partial protonation of the amide moiety, inducing rapid κ²-N,N to κ²-N,O ligand isomerization. Consistently, DFT modeling on the simpler complex 1 showed that the κ²-N,N key intermediate of FA dehydrogenation ( I_NH ), bearing a N-protonated pica, can easily transform into the κ²-N,O analogue ( I_NH2 ; ΔG^≠≈11 kcal mol⁻¹, ΔG ≈−5 kcal mol⁻¹). Intramolecular hydrogen liberation from I_NH2 is predicted to be rather prohibitive (ΔG^≠≈26 kcal mol⁻¹, ΔG≈23 kcal mol⁻¹), indicating that FA dehydrogenation should involve mostly κ²-N,N intermediates, at least at relatively high pH. Under FA dehydrogenation conditions, 2 was progressively consumed, and the vast majority of the Ir centers (58 %) were eventually found in the form of Cp*-complexes with a pyridine-amine ligand. This likely derived from hydrogenation of the pyridine-carboxiamide via a hemiaminal intermediate, which could also be detected. Clear evidence for ligand hydrogenation being the main degradation pathway also for 1 was obtained, as further confirmed by spectroscopic and catalytic tests on the independently synthesized degradation product 1 c . DFT calculations confirmed that this side reaction is kinetically and thermodynamically accessible.     

Reversible Photothermal Isomerization of Carborane-Fused Azaborole to Borirane: Synthesis and Reactivity of Carbene-Stabilized Carborane-Fused Borirane

A fully reversible photothermal isomerization between carborane-fused trigonal-planar azaborole (dark-purple) and tetrahedral borirane (pale-yellow) has been observed, leading to the isolation and structural characterization of the first example of carborane-fused borirane. DFT calculations indicate that the azaborole is thermodynamically more stable than the borirane by 11.2 kcal mol⁻¹, and the energy barrier for the thermal conversion from azaborole to borirane is 35.5 kcal mol⁻¹. The reactivity studies show that the B−C(cage) bond in borirane can be broken in the reaction with CuCl, HCl, or elemental sulfur.     

A theoretical study of C4H5N isomers: Comparison of cyano and isocyano as substituents

Ab initio molecular orbital calculations using a 3-21G basis set have been used to optimize geometries for pyrrole, CH₃(X)CCH₂, CH₃(H)CCHX (both cis and trans), c-C₃H₅X, and CH₂CHCH₂X, where X is CN and NC. In all the alkenyl derivatives methyl groups are found to adopt the conformation in which the methyl hydrogen eclipses the double bond. 6-31G*∥3-21G level calculations show the alkenyl cyanides to be of similar energy to pyrrole, but the isocyanides are ～20 kcal mol^?1 higher in energy. For both substituents the cyclopropyl derivatives are higher in energy by ～10 kcal mol^?1. At the 6-31G* level ring strain is 27.7 kcal mol^?1 for the cyanide and 30.6 kcal mol^?1 for the isocyanide. Data on the relative energies of RCN and RNC are compared when R is (i) a saturated hydrocarbon, (ii) an unsaturated hydrocarbon, (iii) an α-carbenium ion, (iv) an allyl cation, and (v) an α-carbanion.     

Rotational isomerism involving an acetylenic carbon. Part 5: Restricted rotation about acetylenic axis in sterically crowded bis(1-phenyl-9-anthryl)ethynes

The title sterically crowded di-9-anthrylethyne derivative with 3,5-ⁱPr₂-phenyl groups at 1-position showed a barrier to rotation about the acetylenic axis of 18.0 kcal mol⁻¹ based on a dynamic NMR study, which is an extremely high value for acyclic diarylethynes. The mechanism of the dynamic stereochemistry and the substituent effect on the rotational barrier are discussed.     

A Highly Oxidizing and Isolable Oxoruthenium(V) Complex [RuV(N4O)(O)]2+: Electronic Structure,Redox Properties,and Oxidation Reactions Investigated by DFT Calculations

The electronic structure and redox properties of the highly oxidizing, isolable Ru^V?O complex [Ru^V(N₄O)(O)]²⁺, its oxidation reactions with saturated alkanes (cyclohexane and methane) and inorganic substrates (hydrochloric acid and water), and its intermolecular coupling reaction have been examined by DFT calculations. The oxidation reactions with cyclohexane and methane proceed through hydrogen atom transfer in a transition state with a calculated free energy barrier of 10.8 and 23.8 kcal mol^?1, respectively. The overall free energy activation barrier (ΔG^≠=25.5 kcal mol^?1) of oxidation of hydrochloric acid can be decomposed into two parts: the formation of [Ru^III(N₄O)(HOCl)]²⁺ (ΔG=15.0 kcal mol^?1) and the substitution of HOCl by a water molecule (ΔG^≠=10.5 kcal mol^?1). For water oxidation, nucleophilic attack on Ru^V?O by water, leading to O? O bond formation, has a free energy barrier of 24.0 kcal mol^?1, the major component of which comes from the cleavage of the H? OH bond of water. Intermolecular self‐coupling of two molecules of [Ru^V(N₄O)(O)]²⁺ leads to the [(N₄O)Ru^IV? O₂? Ru^III(N₄O)]⁴⁺ complex with a calculated free energy barrier of 12.0 kcal mol^?1.