AB initio study of thermodynamic stability and structure of cage molecules B4N4H8 and Be4O4H8

Stable molecular structures of heterocubane systems B₄N₄H₈ 2 and Be₄O₄H₈, isoelectronic to the cubane molecule, are investigated by ab initio (RHF/6-31G**, MP2(full)/6-31C**, and MP2(full)/6-311+ + G**) methods and are shown to be highly thetmodynamically stable. Decomposition of structure 2 into two 1,3,2,4-diazadiboroethidine molecules 6 or four iminobomne NBNH molecules 11 is an endothermal process taking 10.1 (RHF/6-31G**), 39.6 (MP2(full)/6-31G**) kcaUmole and 140.6 (RHF/6-31G**), 161.4 (MP2(full)/6-31G**) kcal/mole, respectively. Decomposition of structure 3 into two 1,3,2,4-dioxydi-beryllothidine molecules 12 or four molecules 13 is also an endothermal reaction taking 22.1 (RHF/6-31G**), 39.8 (MP2(full)/6-31G**) kcal/mole and 127.1 (RHF/6-31G**), 155.2 (MP2(full)/631G**) kcal/mole, respectively. The geometrical characteristics of simple molecules BeH₂ 15, Be₂ 16 and 17, Be₂H₂ 18, Be₂H₄ 19, BeO 20, and Be₂O₂ 21 are calculated. Translated from Zhumal Struktumoi Khim ii, Vol. 41, No. 1, pp. 3-13, January–February, 2000     

Quantum-Chemical Study of Electronic and Steric Structure of Vinyltetrazoles: I. 2-Substituted 5-Vinyltetrazoles

The total Mulliken charges on the carbon atoms of the vinyl group, populations of S-trans-(N¹)conformers, and internal rotation energies were calculated ab initio (HF/6-31G**, MP2/6-31G**, and MP2/6-31G**//AM1) for a series of 2R-5-vinyltetrazoles (R = CH₃, C₂H₅, i-C₃H₇, t-C₄H₉, C₆H₅). The calculation results were compared to the available experimental data.     

Stable conformations of CH3CH2OCH2CH2OH: A comparison of theoretical methods

This article presents the results of an extensive examination of the stable conformations of CH₃CH₂OCH₂CH₂OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.     

Quantum-Chemical Study of the Electronic and Steric Structure of Vinyltetrazoles: II. 2-Vinyltetrazoles

The total Mulliken charges on the C and N atoms, populations of the S-trans-(N¹) conformers, and rotation barriers in the molecules of 2-vinyl-5-R-tetrazoles (R = H, CH₃, CH = CH₂, C₆H₅, CH₂Cl, CF₃) were calculated ab initio (HF/6-31G**, MP2/6-31G**). The results were compared with the ¹H and ¹³C NMR data for these compounds.     

Semi-Empirical and DFT Studies on Structures and Spectra for C78（CH2）2

Eighteen possible isomers of C78（CH2）2 weTe investigated by the INDO method. It was indicated that the most stable isomer was 42,43,62,63-C78（CH2）2, where the -CH2 groups were added to the 6/6 bonds located at the same hexagon passed by the longest axis of C78 （C2v）, to form cyclopropane structures. Based on the most stable four geometries of C78（CH2）2 optimized at B3LYP/3-21G level, the first absorptions in the electronic spectra calculated with the INDO/CIS method and the IR frequencies of the C-C bonds on the carbon cage computed using the AM1 method were blue-shifted compared with those of C78 （C2v） because of the bigger LUMO-HOMO energy gap and the less conjugated carbon cage after the addition. The chemical shifts of ^13C NMR for the carbon atoms on the added bonds calculated at B3LYP/3-21G level were moved upfield thanks to the conversion from sp^2-C to sp^3-C.     

Conformational analysis of 2-methyl-5-nitro-1,3,2-dioxaborinane

Quantum-chemical methods HF/6-31G(d), HF/6-31+G(d), MP2/6-31G(d)//HF/6-31G(d), and MP2/6-31+G(d)//HF/6-31+G(d) were used to investigate the conformational isomerization of 2-methyl-5-nitro-1,3,2-dioxaborinane. It has been shown that a potential energy surface of this compound includes two minima: an axial form of semi-chair and equatorial sofa together with a transition state belonging to the conformation of 2,5-twist-form. A comparison between experimental NMR ¹H and theoretical vicinal coupling constants was used to determine the quantitative conformational composition of cyclic boric acid ester and a value of ΔG ⁰ for nitro group at the ring carbon atom C⁵ in CCl₄ and C₆D₅NO₂ solutions.     

The fragmentations of [M-H]- anions derived from underivatised peptides. The side-chain loss of H2S from Cys. A joint experimental and theoretical study

Loss of H₂S is the characteristic Cys side‐chain fragmentation of the [M? H]^? anions of Cys‐containing peptides. A combination of experiment and theory suggests that this reaction is initiated from the Cys enolate anion as follows: RNH‐^?C(CH₂SH)CONHR′ Ø [RNHC(?CH₂)CONHR′ (HS^?)] Ø [RNHC(?CH₂)CO‐HNR′‐H]^?+H₂S. This process is facile. Calculations at the HF/6‐31G(d)//AM1 level of theory indicate that the initial anion needs only ≥20.1 kcal mol^?1 of excess energy to effect loss of H₂S. Loss of CH₂S is a minor process, RNHCH(CH₂SH)CON^?‐R′ Ø RNHCH(CH₂S^?)CONHR′ Ø RNH ^?CHCONHR+CH₂S, requiring an excess energy of ≥50.2 kcal mol^?1. When Cys occupies the C‐terminal end of a peptide, the major fragmentation from the [M–H]^? species involves loss of (H₂S+CO₂). A deuterium‐labelling study suggests that this could either be a charge‐remote reaction (a process which occurs remote from and uninfluenced by the charged centre in the molecule), or an anionic reaction initiated from the C‐terminal CO₂^? group. These processes have barriers requiring the starting material to have an excess energy of ≥79.6 (charge‐remote) or ≥67.1 (anion‐directed) kcal mol^?1, respectively, at the HF/6‐31G(d)//AM1 level of theory. The corresponding losses of CH₂O and H₂O from the [M? H]^? anions of Ser‐containing peptides require ≥35.6 and ≥44.4 kcal mol^?1 of excess energy (calculated at the AM1 level of theory), explaining why loss of CH₂O is the characteristic side‐chain loss of Ser in the negative ion mode. Copyright © 2003 John Wiley & Sons, Ltd.     

A combined theoretical and experimental approach to the unimolecular loss of molecular hydrogen from protonated formaldehyde: Determination of the average internal energy of metastable [CH2OH]+ ions

Ab initio quantum chemical calculations (MP2/4–31G**) were performed for the dihydrogen elimination reaction from protonated formaldehyde. The energy difference between reactants and products and the activation energies were found to be in good agreement with the corresponding experimental quantities. Theoretical rate vs. energy curves were computed for a series of isotopic variants of the reaction using the Rice–Ramsperger–Kassel–Marcus (RRKM) method. The vibrational frequencies used in these calculations were taken from the 4–31G** geometry-optimized transition state and reactant structures. Quantum mechanical tunnelling was introduced to explain the existence of metastable CH₂OH ions, and a negative kinetic shift of about 0.1 eV was found. The intramolecular kinetic isotope effect for loss of HH/HD and DH/DD was calculated and compared with the experimental data. The result is consistent with the assumption that the average internal energy of metastable [CH₂OH]⁺ ions is very close to the critical energy for H₂ loss.     

Diagnostic cyclisation reactions which follow phosphate transfer to carboxylate anion centres for energised [M-H]- anions of pTyr-containing peptides

The low‐energy negative ion phosphoTyr to C‐terminal ‐CO₂PO₃H₂ rearrangement occurs for energised peptide [M–H]^– anions even when there are seven amino acid residues between the pTyr and C‐terminal amino acid residues. The rearranged C‐terminal ‐CO₂PO₂H(O^–) group effects characteristic S_Ni cyclisation/cleavage reactions. The most pronounced of these involves the electrophilic central backbone carbon of the penultimate amino acid residue. This reaction is aided by the intermediacy of an H‐bonded intermediate in which the nucleophilic and electrophilic reaction centres are held in proximity in order for the S_Ni cyclisation/cleavage to proceed. The ΔG_reaction is +184 kJ mol^?1 with the barrier to the S_Ni transition state being +240 kJ mol^?1 at the HF/6‐31 + G(d)//AM1 level of theory. A similar phosphate rearrangement from pTyr to side chain CO₂^– (of Asp or Glu) may also occur for energised peptide [M–H]^– anions. The reaction is favourable: ΔG_reaction is ?44 kJ mol^?1 with a maximum barrier of +21 kJ mol^?1 (to the initial transition state) when Asp and Tyr are adjacent. The rearranged species R¹‐Tyr‐NHCH(CH₂CO₂PO₃H^–)COR² (R¹ = CHO; R² = OCH₃) may undergo an S_Ni six‐centred cyclisation/cleavage reaction to form the product anion R¹‐Tyr(NH^–). This process has a high energy requirement [ΔG_reaction = +224 kJ mol^?1, with the barrier to the S_Ni transition state being +299 kJ mol^?1]. Copyright © 2011 John Wiley & Sons, Ltd.     

Structures and stability of N9, N9 − and N9 + clusters

 Ab initio molecular orbital calculations for N₉, N⁻ ₉ and N⁺ ₉ isomers were carried out at the HF/ 6-31G*, B3PW91/6-31G*, B3LYP/6-31G* and MP2/ 6-31G* levels of theory. Stable equilibrium geometric structures were determined by harmonic vibrational frequency analyses at the HF/6-31G*, B3PW91/6-31G* and B3LYP/6-31G* levels of theory. The most stable free-radical N₉ cluster is structure 1 with C _{2 v} symmetry and that of anion N⁻ ₉ is structure 3 with C _s symmetry. Only one stable structure of the N⁺ ₉ cation with C _{2 v} symmetry was predicted. Their potential application as high-energy-density materials has been examined. Received: 15 June 1999 / Accepted: 11 October 1999 / Published online: 14 March 2000     

High level ab initio and density functional theory calculations of the dissociation energies,ionization energies,geometrical variations,and vibrational modes of ground and excited CO2, CO2+, and CO22+

The potential energy surface of CO₂²⁺ ( ³Σ_g^?) is investigated with HF, MP2, MP4, CBS‐Q, G1, G2MP2, G2, G3B3, and B3LYP/6‐311++G(3df,3pd) methods. Density functional theory shows the lowest dissociation channel of this compound to be the formation of CO⁺ ( ²Σ⁺)+O⁺ ( ⁴S_u) and to have a barrier of around 2 eV as well as a dissociation energy of around ?3.2 eV. Thus we propose that with enough correlation it is possible to accurately predict the energies of dissociation and barrier widths and heights to test for the stability of a particular molecular species. We also propose a refinement of current understanding by observing HOMO–LUMO gaps, Lowdin and Mulliken bond orders (to test for bond orbital overlap and hence qualitatively describe bonding and fragmentation in these complexes) and predicted spectrum for such studies as ZEKE spectroscopy (to study cationic states) and REMPI (to study the first excited states) of these class of molecules and, we hope, provide future insight into larger and more interesting systems. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Methanediol decomposition mechanisms: A study considering various ab initio approaches

The alternative decomposition reactions CH₂(OH)₂ → CH₂O + H₂O and CH₂(OH)₂ + H₂O → CH₂O + 2H₂O are investigated using the semiempirical PM 3 as well as the ab initio HF /3-21G , HF /6-31G , HF /6-31G **, and MP 2/6-31G ** calculations. Reactants, products, and appropriate transition states are located on corresponding potential energy surfaces and compared with those reported in earlier studies. © 1996 John Wiley & Sons, Inc.     

Theoretical investigation of ion pair SN2 reactions of alkali isothiocyanates with alkyl halides. Part 1. Reaction of lithium isothiocyanate and methyl fluoride with inversion mechanism

The gas‐phase ionic S_N2 reactions NCS^‐ + CH₃F and ion pair S_N2 reaction LiNCS + CH₃F with inversion mechanism were investigated at the level of MP2(full)/6‐311+G**//HF/6‐311+G**. Both of them involve the reactants complex, inversion transition state, and products complex. There are two possible reaction pathways in the ionic S_N2 reaction but four reaction pathways in the ion pair S_N2 reaction. Our results indicate that the introduction of lithium significantly lower the reaction barrier and make the ion pair displacement reaction more facile. For both ionic and ion pair reaction, methyl thiocyanate is predicted to be the major product, but the latter is more selective. More‐stable methyl isothiocyanate can be prepared by thermal rearrangement of methyl thiocyanate. The theoretical predictions are consistent with the known experimental results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Reactivity study on morpholine‐1‐carbothioic acid (2‐phenyl‐3H‐quinazolin‐4‐ylidene) amide

Regioselective reactions of morpholine‐1‐carbothioic acid (2‐phenyl‐3H‐quinazolin‐4‐ylidene) amide ( 1 ) with electrophiles and nucleophiles were studied. The compound ( 1 ) reacts with alkyl halides in basic medium to afford S‐substituted isothiourea derivatives, with amines to give 1,1‐disubstituted‐3‐(2‐phenyl‐3H‐quinazolin‐4‐ylidene) thioureas and l‐substituted‐3‐(2‐phenyl‐quinazolin‐4‐yl) thioureas via transami‐nation reaction. The reaction of ( 1 ) with amines in the presence of H₂O₂ provided N⁴‐disubstituted‐N'⁴‐(2‐phenylquinazolin‐4‐yl)morpholin‐4‐carboximidamide via oxidative desulfurization. Estimation of reactivity sites on ( 1 ) was supported using the ab initio (HF/6‐31G**) quantum chemistry calculations. The ir, ¹H nmr, ¹³C nmr, mass spectroscopy and x‐ray identified the isolated products.     

A theoretical study of the condensation reactions of methyl cation with ammonia,water, hydrogen fluoride and hydrogen sulphide

Ab initio molecular orbital calculations have been used to study the condensation reactions of CH₃^? with NH₃, H₂O, HF and H₂S. Geometry optimization has been carried out at the Hartree—Fock (HF) level with the split-valence plus d-polarization 6-31G* basis set and improved relative energies obtained from calculations which employ the split-valence plus dp-polarization 6-31G** basis set with electron correlation incorporated via Moller—Plesset perturbation theory terminated at third order (MP3). Zero-point vibrational energies have also been determined and taken into account in deriving relative energies. The structures of the intermediates CH₃XH^? (X = NH₂, OH, F and SH) have been obtained and dissociation of these intermediates into CH₂X⁺ + H₂ on the one hand, and CH₃^? + HX on the other, has been examined. It is found that for those species for which the methyl condensation reaction is observed to have an appreciable rate (X = NH₂ and SH), the transition structure for hydrogen elimination from CH₃XH^? lies significantly lower in energy than the reactants CH₃^? + HX (by 75 and 70 kJ mol^?1 respectively). On the other hand, for those species for which the methyl condensation reaction is not observed (X = OH and F), the transition structure for H₂ elimination lies higher in energy than CH₃^? + HX (by 6 and 87 kJ mol^?1 respectively).     

Molecular Structure of Tetrahydroxycalix[4]arene [-(C<Subscript>6</Subscript>H<Subscript>3</Subscript>OH)-CH<Subscript>2</Subscript>-]<Subscript>4</Subscript> in the Gas Phase

Gas-phase electron diffraction and HF/6-31G*, HF/6-31G**, and B3LYP/6-31G* ab initio calculations were used to find that in the gas phase at 242°C the calix[4]arene [-(C₆H₃OH)-CH₂-]₄ molecule possesses a C₄ conformation. Geometric parameters of the molecule were determined, and the energies of C-H?O hydrogen bonds (7.3 kcal mol^?1) were estimated by the AM1 method.     

CH3O与ClO双自由基反应机理的量子化学研究

在QCISD(T)/6-311＋G(d,p)//B3LYP/6-311＋G(3df,3pd)水平上, 对CH₃O与ClO双自由基反应进行了理论研究. 结果表明, 该反应共有三个反应通道, 产物分别为HOCl＋CH₂O, CH₂O₂＋HCl和CH₃Cl＋O₂(¹Δ). 不论从动力学角度, 还是从热力学角度看, 形成产物HOCl＋CH₂O的通道均是最有利的, 因此为主要反应通道, 这与实验观察到的结果是一致的.     

Minimal basis set MINI-1 — powerful tool for calculating of molecular interactions. I. Neutral complexes

The Huzinaga MINI-1 minimal basis set was applied to the following complexes: H₃N...HF, H₂O...HF, (HF)₂, (H₂O)₂, HCN...HF, OCO...HF, HF...HNH₂, (HCl)₂, CH₄...OH₂ and (H₃Si)₂O...H₂O. The optimized geometries and stabilization energies agree well with the 6–31G^* values, while the computing time is reduced considerably. The MINI-1 basis set was further tested for the stacking structure of the ethylene dimer and the cyclic structure of the formamide...formamidine complex, where fair agreement with the 4–31G results was obtained. The normal vibrational frequencies calculated for some complexes are comparable to those evaluated at the 4–31G (6–31G) level.     

气相中呋喃负离子与N2O反应机理的理论研究

采用QCISD和MP2两种计算方法,在6-31＋＋G(d,p)的基组下,对气相中呋喃负离子与N2O反应的微观机理进行了较为系统的计算研究。结果表明,通道1中的路径1和2为此反应体系的主反应路径,其各反应驻点的能量均低于反应物的,并且互为竞争路径。主要产物为C4H3NO- 和NO,同时也应能检测到少量的C4H3O2- 和N2。理论计算结果与实验预测基本一致。此外,对于次要路径也做了简要说明,并且此反应体系的所有反应路径均为强放热过程。     

Reaction of photogenerated fluorine atoms with dopant molecules in solid argon

The products of reactions of dopant CH₄ molecules with F atoms diffusing in solid argon at 20–30 K were identified by ESR and FTIR spectroscopy. The F atoms stabilized in the matrix were generated by UV photolysis of Ar?CH₄(CD₄)?F (1000∶1∶1) samples at 13 K. Subsequent heating above 20 K results in thawing off diffusion of the F atoms and formation of products of their reaction with CH₄: radical-molecular complexes^·CH₃?HF (^·CD₃?DF) and radicals^·CH₃ (^·CD₃). The ESR spectra of the radicala are similar to those observed for matrix-isolated^·CH₃. The^·CH₃?HF complexes are characterized by the IR band of HF stetching vibration at 3764 cm^?1. Two additional splittings on the H (a _H·=2 G) and F(a _F=16G) nuclei of the HF molecule appeal in the ESR spectrum of the complex. The latter splitting is retained in the^·CD₃?DF complex, whereA _D· <0.3G The rate constant of the reaction CH₄+F→^·CH₃+HF is equal to ?10^?25 cm³s^?1 at 20 K. Its activation energy (1.7±0.2 kcal mol^?1) is ?0.5 kcal mol^?1 greater than that in the gas phase. The collinear C_3v-configuration of the^·CH₃?HF complex, which is similar to the configuration of the reagents in the transition state of the reaction considered, was established by the comparison of the exprrimental constants of hyperfine coupling with the results of the quantum-chemical calculation.