An ab initio study of the E 3Πg state of the iodine molecule

The E (3)Π(g) state of the iodine molecule is studied by ab initio multireference methods coupled with effective core potentials and large basis sets. Two potential minima are found, a global featuring an ion-pair character, and a local presenting a purely Rydberg nature. Four avoided crossings along the dissociation coordinate attribute an interesting topology to its potential energy curve, and their effect on the vibrational levels of I(2) is discussed.     

Butalene and related compounds: aromatic or antiaromatic?

Density functional theory (DFT) has been used to study the first three members of the condensed cyclobutadienoid series, butalene (3), bicyclobutadienylene (12), and dicyclobutenobutalene (20). The first is planar and is judged "aromatic" by comparisons with suitable models using both energetic and magnetic criteria. The second is nonplanar, and not aromatic, but not so antiaromatic as cyclobutadiene (11). The third is slightly more antiaromatic and best viewed as a butalene fused to two cyclobutadiene rings; its properties are the sum of aromatic and antiaromatic components, like benzocyclobutadiene. Ring-opening transition states for both 3 and 12 have been located, and these are conrotatorily twisted. The ring-opening barrier for 12 is more than twice that for 3. Ring-opening of 20 involves ring inversion as the only barrier.     

An ab initio study of the rotation—vibration energy levels of GeH2 in the ā3B1 state

Thirty-five points on the potential energy surface of the ā³B₁ first excited state for the GeH₂ radical have been calculated using the (ab initio) MRD CI technique. Thirteen parameters in an analytic expression for the potential have been adjusted (by least-squares optimization) so that the surface fits these points. The rotation-vibration energy levels of GeH₂. GeD₂ and GeHD have been calculated using the non-rigid bender Hamiltonian, and we determine for GeH₂ that ν₁ = 1991 cm^-1. ν₂ = 763 cm^-1, and ν₃ = 2012 cm^-1. The equilibrium structure is found to be r_e = 1.545 Å and α_z = 119.8°, and the singlet-triplet splitting is calculated to be 22.8 kcal/mole (7975 cm^-1).     

Comparative semiempirical and ab initio study of the harmonic vibrational frequencies of aniline—I. The ground state

The harmonic vibrational frequencies of the ground state S₀ of aniline obtained from various ab initio methods [6-31G, 6-31G(*) and 6-31G* basis sets] and semiempirical methods (MINDO/3, MNDO, AM1 and PM3) have been compared to the experimental vibrational spectra. Detailed theoretical analyses of the atomic Cartesian displacements of all normal modes are presented. The semiempirical PM3 method reproduces the experimental frequencies of aniline with comparable accuracy to the ab initio methods. Ale PM3 method will be useful in predicting the vibrational spectra of larger aromatic amines.     

Silicon-containing formal 4π-electron four-membered ring systems: antiaromatic, aromatic, or nonaromatic?

Density functional theory calculations (B3LYP) have been carried out to investigate the 4π-electron systems of 2,4-disila-1,3-diphosphacyclobutadiene (compound 1) and the tetrasilacyclobutadiene dication (compound 2). The calculated nucleus-independent chemical shift (NICS) values for these two compounds are negative, which indicates that the core rings of compounds 1 and 2 have a certain amount of aromaticity. However, deep electronic analysis reveals that neither of these two formal 4π-electron four-membered ring systems is aromatic. Compound 1 has very weak, almost negligible antiaromaticity, and the amidinate ligands attached to the Si atoms play an important role in stabilizing this conjugated 4π-electron system. The monoanionic bidentate ligand interacts with the conjugated π?system to cause π-orbital splitting. This ligand-induced π-orbital splitting effect provides an opportunity to manipulate the gap between occupied and unoccupied π?orbitals in conjugated systems. Conversely, compound 2 is nonaromatic because its core ring does not have a conjugated π?ring system and does not fulfill the requirements of a Hückel system.     

Does the interconversion of polysulfur compounds proceed via hypervalent intermediates? An ab initio MO study

Ab initio MO calculations at the CCSD(T)/6-311++G(2df,p)//MP2/6-311++G** level have been carried out to determine the reaction energies and Gibbs energies of the homolytic dissociation of the S-S bonds in the chainlike sulfanes H2Sn (n = 2-4). Good agreement with the experimental data is observed. At the same level of theory, the formation of the hypothetical sulfuranes H2S(SH)2, H2S(SSH)2, and S(SH)4 from H2S and the mentioned sulfanes has been studied. Species of this type had been proposed as intermediates in the interconversion reactions of polysulfur compounds (e.g., formation of S7 from S8 and vice versa). The three sulfuranes serve here as model compounds. On the basis of the Gibbs energies and activation energies at 298 K, it is shown that the formation of the three sulfuranes from sulfanes requires too much energy and activation energy to successfully compete with homolytic dissociation reactions. In addition, the formation of the methylsubstituted sulfurane S(SMe)4 from the sulfanes Me2S2 and Me2S3 was studied to elucidate the mechanism of the formal exchange of sulfur atoms between polysulfane molecules. However, both the reaction energy of 199 kJ mol(-1) and the activation energy of 287 kJ mol(-1), calculated at the MP2/6-31G* level, are much higher than the homolytic dissociation energy of the S-S bonds in chain- and ringlike polysulfur compounds, such as Me2S4 (140 kJ mol(-1)) and sulfur homocycles (150 kJ mol(-1)). Therefore, it is concluded that the observed interconversion reactions of sulfur rings and of chainlike polysulfanes do not proceed via sulfurane-type intermediates. Instead, these reactions will take place by a radical chain mechanism at high temperatures, while at temperatures below 100 degrees C they are most probably initiated either by traces of nucleophiles that are present as impurities or by the polar surface groups usually present on the walls of the vessels used.     

An ab initio MO study on the direct and migratory reaction mechanism for the formation of HF in H+ClF system

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Reactions that generate aromatic molecules: is aromatic stabilization less or more advanced than bond changes at the transition state? Kinetic and thermodynamic acidities of rhenium carbene complexes

A kinetic study of the reversible deprotonation of the rhenium carbene complexes 1H(+)(O), 1H(+)(S) and 2H(+)(O) by carboxylate ions, primary aliphatic and secondary alicyclic amines, water and OH(-) in 50% MeCN-50% water (v/v) at 25 degrees C is reported. These carbene complexes are of special interest because in their deprotonated form they represent derivatives of the aromatic heterocycles furan, thiophene and benzofuran. Intrinsic rate constants (k(o) for Delta G degrees = 0) determined from appropriate Br?nsted plots for these rhenium carbene complexes and for the corresponding selenophene (1H(+)(Se)) and benzothiophene (2H(+)(S)) derivatives investigated earlier follow the orders furan < selenophene < thiophene and benzofuran less, similar benzothiophene. These orders indicate that an increase in aromaticity leads to an increase in the intrinsic rate constant or a decrease in the intrinsic barrier. This is an unexpected result; it implies that, in contrast to common resonance effects, the development of aromaticity at the transition state is ahead of proton transfer, i.e., the percentage development of the aromatic stabilization energy at the transition state is higher than the percentage of proton transfer.     

The aromatic diboracyclopropenyl (diboriranyl) anion; CB2H3 −: An ab initio study

The most stable structure of CB₂H₃ ^–, as established computationally, is the aromatic diboracyclopropenyl (diboriranyl) anion (5), while open-chainC _2v, isomer H₂BCBH (7) is only 3 kcal/mol higher in energy at the QCISD(T)/6-311 +G^**//MP2/6-31+G^*+ZPE (HF/6-31 +G^*). The 47-kcal/mol barrier between cyclic,5, and open-chain,7, structures suggests that both of them may be observed. The aromatic stabilization energy of the diboriranyl anion (18 kcal/mol) is half the value in the isoelectronic cyclopropenium ion, C₃H₃ ⁺. The computed, by IGLO method (5a), and experimental (6a) chemical shifts,(¹³C) and(¹¹B), agree within 4 ppm range. The theoretical vibrational frequencies of the most stable isomers,5 and7, are presented for experimental verification of these species.     

How stable is a collagen triple helix? An ab initio study on various collagen and β‐sheet forming sequences

Collagen forms the well characterized triple helical secondary structure, stabilized by interchain H-bonds. Here we have investigated the stability of fully optimized collagen triple helices and beta-pleated sheets by using first principles (ab initio and DFT) calculations so as to determine the secondary structure preference depending on the amino acid composition. Models composed of a total of 18 amino acid residues were studied at six different amino acid compositions: (i) L-alanine only, (ii) glycine only, (iii) L-alanines and glycine, (iv) L-alanines and D-alanine, (v) L-prolines with glycine, (vi) L-proline, L-hydroxyproline, and glycine. The last two, v and vi, were designed to mimic the core part of collagen. Furthermore, ii, iii, and iv model the binding and/or recognition sites of collagen. Finally, i models the G-->A replacement, rare in collagen. All calculated structures show great resemblance to those determined by X-ray crystallography. Calculated triple helix formation affinities correlate well with experimentally determined stabilities derived from melting point (T(m)) data of different collagen models. The stabilization energy of a collagen triple helical structure over that of a beta-pleated sheet is 2.1 kcal mol(-1) per triplet for the [(-Pro-Hyp-Gly-)(2)](3) collagen peptide. This changes to 4.8 kcal mol(-1) per triplet of destabilization energy for the [(-Ala-Ala-Gly-)(2)](3) sequence, known to be disfavored in collagen. The present study proves that by using first principles methods for calculating stabilities of supramolecular complexes, such as collagen and beta-pleated sheets, one can obtain stability data in full agreement with experimental observations, which envisage the applicability of QM in molecular design.     

Effect on ring current of the Kekulé vibration in aromatic and antiaromatic rings

Derivative current-density maps are used to follow the changes in ring-current (and hence, on the magnetic criterion, the changes in aromaticity) with the Kekulé vibrations of the prototypical aromatic, antiaromatic, and nonaromatic systems of benzene, cyclooctatetraene (COT), and borazine. Maps are computed at the ipsocentric CHF/6-31G**//RHF/6-31G** level. The first-derivative map for benzene shows a growing-in of localized bond currents, and the second-derivative map shows a pure, paratropic "antiring-current", leading to the conclusion that vibrational motion along the Kekulé mode will reduce the net aromaticity of benzene, on average. For planar-constrained D(4h) COT, the Kekulé mode (positive for reduction of bond-length alternation) increases paratropicity at both first and second order, indicating an average increase in antiaromaticity with zero-point motion along this mode. On the ring-current criterion, breathing expansions of benzene and D(4h) COT reduce aromaticity and increase antiaromaticity, respectively.     

Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path

The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative stability to ΔE(ZPE) = (0.51 ± 0.08) kcal mol(-1). A scheme is also suggested to model the full-dimensional isomerization potential-energy surface using a quadratic expansion that is parametrically represented by a Fourier analysis in the torsion angle. The method illustrated at the raw and complete basis-set limit coupled-cluster levels can provide a valuable tool for a future analysis of the available (incomplete thus far) experimental rovibrational data.     

The transition probabilities from the ground state to the excited J = 0 1Σu(+) levels of H2: measurements and ab initio quantum defect study

The energies, widths and absolute intensities of the P(1) v' = 0, J' = 1 absorption transitions of H(2) have been measured in the spectral range of 81-75 nm using monochromatized synchrotron radiation. This work completes and extends previous observations, in particular those of Herzberg and Jungen [J. Mol. Spectrosc. 41, 425 (1972)]. Ab initio multichannel quantum defect theory (MQDT) is used to corroborate the spectral analysis of the experimental data. Line intensities and decay widths are also calculated using MQDT.     

A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization?

In this work we present a detailed analysis of the activation free energies and averaged interactions for the Claisen and Cope rearrangements of chorismate and carbachorismate catalyzed by Bacillus subtilischorismate mutase (BsCM) using quantum mechanics/molecular mechanics (QM/MM) simulation methods. In gas phase, both reactions are described as concerted processes, with the activation free energy for carbachorismate being about 10-15 kcal mol(-)(1) larger than for chorismate, at the AM1 and B3LYP/6-31G levels. Aqueous solution and BsCM active site environments reduce the free energy barriers for both reactions, due to the fact that in these media the two carboxylate groups can be approached more easily than in the gas phase. The enzyme specifically reduces the activation free energy of the Claisen rearrangement about 3 kcal mol(-)(1) more than that for the Cope reaction. This result is due to a larger transition state stabilization associated to the formation of a hydrogen bond between Arg90 and the ether oxygen. When this oxygen atom is changed by a methylene group, the interaction is lost and Arg90 moves inside the active site establishing stronger interactions with one of the carboxylate groups. This fact yields a more intense rearrangement of the substrate structure. Comparing two reactions in the same enzyme, we have been able to obtain conclusions about the relative magnitude of the substrate preorganization and transition state stabilization effects. Transition state stabilization seems to be the dominant effect in this case.     

What is the unperturbed state in polymer solutions?

We report theoretical results about amphiphilic random copolymers in a quasi‐ideal conformation with an overall size very close to that of the analogue homopolymers. We found that a few states may coexist with about the same free energy and a similar radius of gyration, but with different intramolecular conformations. We also argue that, in most cases, amphiphilic copolymers may never achieve the unperturbed Θ state, defined thermodynamically by a vanishing second virial coefficient. Thus, we suggest that such copolymers usually show neither an unperturbed conformation nor an unperturbed state from the thermodynamic viewpoint. We also briefly discuss star homopolymers, which show a depression of the Θ temperature with respect to linear chains and a significant, though finite, Θ swelling, as well as linear chains in the Θ state and in the melt. The main general conclusion is that interactions between chain segments do not cancel each other and are non‐negligible. Accordingly, we suggest that the word "unperturbed" be used only with reference to solution thermodynamics and not for the chain size or conformation.     

Role of the 3(ππ*) state in photolysis of lumisantonin: insight from ab initio studies

The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways. Calculations indicate that the (1)(nπ*) state is the accessible low-lying singlet state with a notable oscillator strength under an excitation wavelength of 320 nm and that it can effectively decay to the (3)(ππ*) state through intersystem crossing in the region of minimum surface crossings with a notable spin-orbital coupling constant. The (3)(ππ*) state, derived from the promotion of an electron from the π-type orbital mixed with the σ orbital localized on the C-C bond in the three-membered alkyl ring to the π* orbital of conjugation carbon atoms, plays a critical role in C-C bond cleavage. Based on the different C-C bond rupture patterns, the reaction pathways can be divided into paths A and B. Photolysis along path A arising from C1-C5 bond rupture is favorable because of the dynamic and thermodynamic preferences on the triplet excited-state PES. Path B is derived from the cleavage of the C5-C6 bond, leading first to a relatively stable species, compared to intermediate A-INT formed on the ground state PES. Accordingly, path B is relatively facile for the pyrolytic reaction. The present results provide a basis to interpret the experimental observations.     

Is the structure of hydroxide dihydrate OH−(H2O)2? An ab initio path integral molecular dynamics study

We carried out ab initio path integral molecular dynamics simulations at room temperature for OH^?(H₂O) _n (n = 1, 2) clusters to elucidate the ionic hydrogen bond structure with full thermal and nuclear quantum effects. We found that the hydrogen-bonded proton is located near the water molecule in the case of n = 2, while the proton is located at the center between hydroxide ion and the water molecule in the case of n = 1. Thus, the solvated hydroxide structure \({\text{HO}}{-}{\text{H}} \cdots{\text{OH}}\) is found in n = 2, while the proton sharing hydroxide structure \({\text{HO}} \cdots {\text{H}} \cdots {\text{OH}}\) is in n = 1. We found that the nature of hydrogen bonds significantly changes with the number of water molecules around the hydroxide. We also compared these results with those of F^?(H₂O) _n (n = 1, 2) clusters.