Nature of the interaction between ammonia derivatives and carbon disulfide. A theoretical investigation

The interactions between NH₃, its methylated and chlorinated derivatives and CS₂ are investigated by ab initio CCSD(T) and density functional BLYP‐D3 methods. The CCSD(T)/aug‐cc‐pVTZ calculated interaction energies of complexes characterized by the S···N chalcogen bonds range between ?1.71 and ?2.78 kcal mol^?1. The S···N bonds are studied by atoms in molecules, natural bond orbital, and noncovalent interaction methods. The lack of correlation between the interaction energies of methylated amines complexes and the electrostatic potential results from the lone pair effect in aliphatic amines. Different structures of CS₂ complexed with ammonia derivatives, stabilized by other than the S···N chalcogen bonds, are also predicted. These structures are characterized by interaction energies ranging between 1.15 and 3.46 kcal mol^?1. The results show that the complexing ability of CS₂ is not very high but this molecule is able to attack the electrophilic or nucleophilic sites of a guest molecule.     

Variational transition‐state theory study of the atmospheric reaction OH + O3 → HO2 + O2

We report variational transition‐state theory calculations for the OH + O₃→ HO₂ + O₂ reaction based on the recently reported double many‐body expansion potential energy surface for ground‐state HO₄ [Chem Phys Lett 2000, 331, 474]. The barrier height of 1.884 kcal mol^?1 is comparable to the value of 1.77–2.0 kcal mol^?1 suggested by experimental measurements, both much smaller than the value of 2.16–5.11 kcal mol^?1 predicted by previous ab initio calculations. The calculated rate constant shows good agreement with available experimental results and a previous theoretical dynamics prediction, thus implying that the previous ab initio calculations will significantly underestimate the rate constant. Variational and tunneling effects are found to be negligible over the temperature range 100–2000 K. The O₁? O₂ bond is shown to be spectator like during the reactive process, which confirms a previous theoretical dynamics prediction. © 2007 Wiley Periodicals, Inc. 39: 148–153, 2007     

An ab initio molecular orbital study of the potential energy surface of the N2H → N2 + H system

The N₂H potential energy surface has been examined by ab initio molecular orbital theory using the 6-31G^** basis set with correlation energy evaluated by Møller—Plesset perturbation theory to fourth order. The ΔE for N₂H → N₂ + H is ?14.4 kcal mol^?1 and the barrier to dissociation is 10.5 kcal mol^?1. Inclusion of zero-point vibrational energies reduces the barrier to 5.8 kcal mol^?1.     

The role of internal H-bonding in the conformational preferences of some molecules of the formula CH3CHYCH2X

The conformational energies of 1-amino-2-propanol, 2-amino-1-propanol and 1,2-diaminopropane are studied using ab initio molecular orbital theory employing minimal (STO-3G) and extended (4-31G) basis sets. Calculations at both levels of theory generally favor conformations stabilized by internal H-bonding for all molecules considered. Results are first presented for conformations employing assumed geometries. Since the conformational energy differences as found by the initial set of calculations are in some cases rather small it then becomes necessary to introduce geometry optimizations into the study at the minimal STO-3G level. In addition, to get a better estimate of the energy differences of the various conformations 4-31G calculations are performed on the STO-3G optimized structures. These latter results indicate the following, (a) For 1-amino-2-propanol only one conformation that is stabilized by intramolecular H-bonding is low in energy; this has the methyl and amino groups anti. The other H-bonded conformer, where the methyl and amino groups are gauche, is predicted to be ca. 1.2 kcal mol^?1 less stable. Similar findings for this molecule have recently been provided by micro-wave spectroscopy. (b) For 2-amino-1-propanol the two H-bonded conformers are only separated by about 0.5 kcal mol^?1, with the anti conformer being more stable. Micro-wave spectroscopy again supports these calculations. (c) For 1,2-diaminopropane the gauche conformer is predicted to be of rather high energy (ca. 2.5 kcal mol^?1) compared to the corresponding anti H-bonded conformer. The value of 2.5 kcal mol^?1should be taken as an upper limit, since the geometry optimization of the gauche conformer of 1,2-diaminopropane is incomplete compared to the optimization carried out for the anti conformer.     

Glyoxal oligomers: A computational study

Ab initio calculations at MP2/6‐311++G(2d,2p) computational level was used to analyze interactions between glyoxal (OCHCHO) dimers and trimers in the gas phase. The structures obtained have been analyzed with the atoms in molecules and natural bond orbital methodologies. Eight minima were located on the potential energy surface of the dimers. Eighteen different structures have been obtained for the trimers. CH···O type of interactions is clustering OCHCHO molecules in studied oligomers. Stabilization energies of dimers and trimers including basis set superposition error and ZPE corrections are in the range 4–8 kJ mol^?1 and 12–19 kJ mol^?1, respectively. Blue shift of CH bond upon complex formation in the ranges between 30–45 and 30–55 cm^?1 was predicted for dimers and trimers, respectively. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Pairing of Isolated Nucleobases: Double Resonance Laser Spectroscopy of Adenine–Thymine

The vibronic spectrum of the adenine–thymine (A–T) base pair was obtained by one‐color resonant two‐photon ionization (R2PI) spectroscopy in a free jet of thermally evaporated A and T under conditions favorable for formation of small clusters. The onset of the spectrum at 35 064 cm^?1 exhibits a large red shift relative to the π–π* origin of 9H‐adenine at 36 105 cm^?1. The IR–UV spectrum was assigned to cluster structures with HNH???O?C/N???HN hydrogen bonding by comparison with the IR spectra of A and T monomers and with ab initio calculated vibrational spectra of the most stable A–T isomers. The Watson–Crick A–T base pair is not the most stable base‐pair structure at different levels of ab initio theory, and its vibrational spectrum is not in agreement with the observed experimental spectrum. Experiments with methylated A and T were performed to further support the structural assignment.     

Ab initio studies on clusters of polar molecules. stability of cyclic versus open-chain trimers of hydrogen fluoride

Large-scale ab initio calculations have been performed on cyclic and open-chain trimers of hydrogen fluoride including partial geometry optimization. The cyclic trimer turned out to be more stable by ≈ 2 kcal/mole. Equilibrium geometries and hydrogen bond energies are compared with corresponding quantities of (HF)₂ and of the infinite chain (HF)∞.     

The Beryllium Pentamer: Trailing an Uneven Sequence of Dissociation Energies

Recent high‐resolution spectroscopic studies by Merritt, Bondybey, and Heaven (Science 2009 , 324, 1548) have heightened the anticipation that small beryllium clusters will soon be observed in the laboratory. Beryllium clusters are important discrete models for the theoretical study of metals. The trigonal bipyramidal Be₅ molecule is studied using high‐level coupled cluster methods. We obtain the optimized geometry, atomization and dissociation energies, and vibrational frequencies. The c～CCSDT(Q) method is employed to compute the atomization and dissociation energies. In this approach, complete basis set (CBS) extrapolations at the CCSD(T) level of theory are combined with an additive correction for the effect of iterative triple and perturbative quadruple excitations. Harmonic vibrational frequencies are obtained using analytic gradients computed at the CCSD(T) level of theory. We report an atomization energy of 129.6 kcal mol^?1 at the trigonal bipyramid global minimum geometry. The Be₅→Be₄+Be dissociation energy is predicted to be 39.5 kcal mol^?1. The analogous dissociation energies for the smaller beryllium clusters are 64.0 kcal mol^?1 (Be₄→Be₃+Be), 24.2 kcal mol^?1 (Be₃→Be₂+Be), and 2.7 kcal mol^?1 (Be₂→Be+Be). The trigonal bipyramidal Be₅ structure has an equatorial–equatorial bond length of 2.000 Å and an axial–equatorial distance of 2.060 Å. Harmonic frequencies of 730, 611, 456, 583, 488, and 338 cm^?1 are obtained at the CCSD(T)/cc‐pCVQZ level of theory. Quadruple excitations are found to make noticeable contributions to the energetics of the pentamer, which exhibits a significant level of static correlation.     

Supramolecular Binding Thermodynamics by Dispersion‐Corrected Density Functional Theory

The equilibrium association free enthalpies ΔG_a for typical supramolecular complexes in solution are calculated by ab initio quantum chemical methods. Ten neutral and three positively charged complexes with experimental ΔG_a values in the range 0 to ?21 kcal mol^?1 (on average ?6 kcal mol^?1) are investigated. The theoretical approach employs a (nondynamic) single‐structure model, but computes the various energy terms accurately without any special empirical adjustments. Dispersion corrected density functional theory (DFT‐D3) with extended basis sets (triple‐ζ and quadruple‐ζ quality) is used to determine structures and gas‐phase interaction energies (ΔE), the COSMO‐RS continuum solvation model (based on DFT data) provides solvation free enthalpies and the remaining ro‐vibrational enthalpic/entropic contributions are obtained from harmonic frequency calculations. Low‐lying vibrational modes are treated by a free‐rotor approximation. The accurate account of London dispersion interactions is mandatory with contributions in the range ?5 to ?60 kcal mol^?1 (up to 200 % of ΔE). Inclusion of three‐body dispersion effects improves the results considerably. A semilocal (TPSS) and a hybrid density functional (PW6B95) have been tested. Although the ΔG_a values result as a sum of individually large terms with opposite sign (ΔE vs. solvation and entropy change), the approach provides unprecedented accuracy for ΔG_a values with errors of only 2 kcal mol^?1 on average. Relative affinities for different guests inside the same host are always obtained correctly. The procedure is suggested as a predictive tool in supramolecular chemistry and can be applied routinely to semirigid systems with 300–400 atoms. The various contributions to binding and enthalpy–entropy compensations are discussed.     

Tetragermacyclobutadiene: Energetically Disfavored with Respect to Its Structural Isomers

Germanium has been a central feature in the renaissance of main‐group inorganic chemistry. Herein, we present the stationary‐point geometries of tetragermacyclobutadiene and its related isomers on the singlet potential energy surface at the CCSD(T)/cc‐pVTZ level of theory. Three of these 12 structures are reported for the first time and one of them is predicted to lie only 0.4 kcal mol^?1 above the previously reported global minimum. Focal‐point analyses has provided electronic energies at the CCSD(T) level of theory, which are extrapolated to the complete basis‐set limit and demonstrate the convergence behavior of the electronic energies with improving levels of theory and increasing basis‐set size. The lowest‐energy structure is the bicyclic structure, which lies 35 kcal mol^?1 below the “all‐Ge” cyclobutadiene structure. The reaction energies for the association of known Ge hydrides (e.g., digermene) to form Ge₄H₄ indicate that Ge₄H₄ could be observed experimentally. We investigate the bonding patterns by examining the frontier molecular orbitals. Our results demonstrate that: 1) the cyclic isomers of (GeH)₄ distort to maximize the mixing of the p orbitals that are involved in the π system of tetragermacyclobutadiene and 2) the lowest‐energy isomers exhibit unusual bonding arrangements (e.g., bridging H bonds) that maximize the nonbonding electron density at the Ge centers.     

A theoretical study of the structures and inversion barriers of CF3− and SiF3−

The structures and inversion barriers of CF₃^? and SiF₃^? have been calculated using ab initio SCF theory with several different basis sets and limited CI. The highest occupied molecular orbital of planar SiF₃^? is shown to have a₁′ symmetry, rather than the normally expected a₂″ symmetry. The best estimates of the inversion barriers are 119 kcal mol^?1 (CF₃^?) and 82 kcal mol ^?1 (SiF₃^?).     

A Mechanistic Study of the Spontaneous Hydrolysis of Glycylserine as the Simplest Model for Protein Self‐Cleavage

A common feature of several classes of intrinsically reactive proteins with diverse biological functions is that they undergo self‐catalyzed reactions initiated by an N→O or N→S acyl shift of a peptide bond adjacent to a serine, threonine, or cysteine residue. In this study, we examine the N→O acyl shift initiated peptide‐bond hydrolysis at the serine residue on a model compound, glycylserine (GlySer), by means of DFT and ab initio methods. In the most favorable rate‐determining transition state, the serine ?COO^? group acts as a general base to accept a proton from the attacking ?OH function, which results in oxyoxazolidine ring closure. The calculated activation energy (29.4 kcal mol^?1) is in excellent agreement with the experimental value, 29.4 kcal mol^?1, determined by ¹H NMR measurements. A reaction mechanism for the entire process of GlySer dipeptide hydrolysis is also proposed. In the case of proteins, we found that when no other groups that may act as a general base are available, the N→O acyl shift mechanism might instead involve a water‐assisted proton transfer from the attacking serine ?OH group to the amide oxygen. However, the calculated energy barrier for this process is relatively high (33.6 kcal mol^?1), thus indicating that in absence of catalytic factors the peptide bond adjacent to serine is no longer a weak point in the protein backbone. An analogous rearrangement involving the amide N‐protonated form, rather than the principle zwitterion form of GlySer, was also considered as a model for the previously proposed mechanism of sea‐urchin sperm protein, enterokinase, and agrin (SEA) domain autoproteolysis. The calculated activation energy (14.3 kcal mol^?1) is significantly lower than the experimental value reported for SEA (≈21 kcal mol^?1), but is still in better agreement as compared to earlier theoretical attempts.     

An ab initio CI investigation of structure and bonding in LiC2H2 complexes

The structures and energies of various LiC₂H₂ complexes have been investigated by means of ab initio molecular orbital calculations. Analytic SCF gradients were employed with a double-ζ basis set to locate and characterize stationary points on the energy surface. Single-point CI calculations using a double-ζ + diffuse and polarization basis set have been carried out at the DZ + P SCF stationary points. With the highest-level theory, the Li—vinylidene complex and the cis bridged adduct are found to be the most favorable arrangements, the former complex being slightly more stable by about 2 kcal mol⁻¹. These molecules are bound respectively by about 5 and 3 kcal mole⁻¹ relative to infinitely separated lithium plus acetylene. Harmonic vibrational frequencies are also reported and confirm the existence of the cis LiC₂H₂ species recently observed in a solid argon matrix.     

Kinetic Stability and Propellant Performance of Green Energetic Materials

A thorough theoretical investigation of four promising green energetic materials is presented. The kinetic stability of the dinitramide, trinitrogen dioxide, pentazole, and oxopentazole anions has been evaluated in the gas phase and in solution by using high‐level ab initio and DFT calculations. Theoretical UV spectra, solid‐state heats of formation, density, as well as propellant performance for the corresponding ammonium salts are reported. All calculated properties for dinitramide are in excellent agreement with experimental data. The stability of the trinitrogen dioxide anion is deemed sufficient to enable synthesis at low temperature, with a barrier for decomposition of approximately 27.5 kcal mol^?1 in solution. Oxopentazolate is expected to be approximately 1200 times more stable than pentazolate in solution, with a barrier exceeding 30 kcal mol^?1, which should enable handling at room temperature. All compounds are predicted to provide high specific impulses when combined with aluminum fuel and a polymeric binder, and rival or surpass the performance of a corresponding ammonium perchlorate based propellant. The investigated substances are also excellent monopropellant candidates. Further study and attempted synthesis of these materials is merited.     

Ab initio study of β-lactam antibiotics. I. Potential energy surface for the amidic CN bond breaking in the β-lactam + OH− reaction

The potential energy surface of the β-lactam + OH^? reaction, related to the mode of action of β-lactam antibiotics, was investigated using the ab initio Hartree—Fock method with the STO-3G basis set. Three possible reaction paths for the B_AC2 breaking of the amidic CN bond were obtained and discussed. The minimum-energy reaction path is characterized by the following processes: (1) the formation of a tetrahedral intermediate, ≈ 121 kcal mol^?1 more stable than the reagents; (2) a barrier, ≈ 15 kcal mol^?1 above the intermediate, which is mainly due to the partial breaking of the amidic bond; (3) the complete breaking of the amidic bond concerted with a proton transfer till the formation of the final product, ≈ 34 kcal mol^?1 more stable than the intermediate. The evolution of some molecular orbitals and of the electron population along the reaction path was also discussed.     

S‐Trifluoromethylation of Thiols by Hypervalent Iodine Reagents: A Joint Experimental and Computational Study

The radical trifluoromethylation of thiophenol in condensed phase applying reagent 1 (3,3‐dimethyl‐1‐(trifluoromethyl)‐1λ³,2‐benziodoxol) has been examined by both theoretical and experimental methodologies. On the basis of ab initio molecular dynamics and metadynamics we show that radical reaction mechanisms favourably compete with polar ones involving the S‐centred nucleophile thiophenol, their free energies of activation, ΔF^≠, lying between 9 and 15 kcal mol^?1. We further show that the origin of the proton activating the reagent is important. Hammett plot analysis reveals intramolecular protonation of 1 , thus generating negative charge on the sulfur atom in the rate‐determining step. The formation of a CF₃ radical can be thermally induced by internal dissociative electron transfer, its activation energy, ΔF^≠, amounting to as little as 10.8 and 2.8 kcal mol^?1 for reagent 1 and its protonated form 2 , respectively. The reduction of the iodine atom by thiophenol occurs either subsequently or in a concerted fashion.     

A theoretical study of the inversion barrier in NF3+

The barrier to inversion in NF⁺₃ has been studied using ab initio molecular-orbital theory including geometry optimization at the correlation energy level. The barrier is predicted to be 12.6 kcal mol⁻¹. Comparison is made to previous theoretical and experimental results.     

Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods

In this study we present the first systematic computational three‐dimensional scan of carbohydrate hydrophobic patches for the ability to interact through CH/π dispersion interactions. The carbohydrates β‐d‐ glucopyranose, β‐d‐ mannopyranose and α‐l‐ fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/π interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC‐DFTB‐D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT‐D BP/def2‐TZVPP level. The results obtained clearly show highly delimited and separated areas around each CH group, with an interaction energy up to ?5.40 kcal mol^?1. The results also show that with increasing H???π distance these delimited areas merge and form one larger region, which covers all hydrogen atoms on that specific carbohydrate side. Simultaneously, the interaction becomes weaker with an energy of ?2.5 kcal mol^?1. All local energy minima were optimized at the DFT‐D BP/def2‐TZVPP level and the interaction energies of these complexes were refined by use of the high‐level ab initio computation at the CCSD(T)/CBS level. Results obtained from the optimization suggest that the CH group hydrogen atoms are not equivalent and the interaction energy at the CCSD(T)/CBS level range from ?3.54 to ?5.40 kcal mol^?1. These results also reveal that the optimal H???π distance for the CH/π dispersion interaction is approximately (2.310±0.030) Å, and the angle defined as carbon‐hydrogen‐benzene geometrical centre is (180±30)°. These results reveal that whereas the dispersion interactions with the lowest interaction energies are quite strictly located in space, the slightly higher interaction energy regions adopt a much larger space.     

Non-empirical calculations on the conformational structure of azobenzene and benzylideneaniline

The conformational structures of cis- and trans-azobenzene and benzylideneaniline have been investigated by means of ab initio SCF calculations. Contrary to semiempirical results, the equilibrium molecular geometries are correctly accounted for in the non-empirical SCF-formalism. Trans-azobenzene is found to be planar, or at least peri-planar, while the phenyl rings of the cis-isomer are twisted by 56° out-of-plane. Both isomers of benzylideneaniline are non-planar, with rotational angles θ₁ (C-N) = 48°, θ₂(C-C) = 0° and θ₁ = θ₂ = 75° for the trans and cis form, respectively. Trans-azobenzene is calculated to be more stable by 10.4 kcal mol^?1 than the cis isomer, which is in good accord with the experimental value of 10 kcal mol^?1. The energy of isomerization of benzylideneaniline amounts to 13.0 kcal mol^?1.     

Oxidative Dehydrogenation of Propane over a VO2‐Exchanged MCM‐22 Zeolite: A DFT Study

The adsorption and the mechanism of the oxidative dehydrogenation (ODH) of propane over VO₂‐exchanged MCM‐22 are investigated by DFT calculations using the M06‐L functional, which takes into account dispersion contributions to the energy. The adsorption energies of propane are in good agreement with those from computationally much more demanding MP2 calculations and with experimental results. In contrast, B3LYP binding energies are too small. The reaction begins with the movement of a methylene hydrogen atom to the oxygen atom of the VO₂ group, which leads to an isopropyl radical bound to a HO? V? O intermediate. This step is rate determining with the apparent activation energy of 30.9 kcal mol^?1, a value within the range of experimental results for ODH over other silica supports. In the propene formation step, the hydroxyl group is the more reactive group requiring an apparent activation energy of 27.7 kcal mol^?1 compared to that of the oxy group of 40.8 kcal mol^?1. To take the effect of the extended framework into account, single‐point calculations on 120T structures at the same level of theory are performed. The apparent activation energy is reduced to 28.5 kcal mol^?1 by a stabilizing effect caused by the framework. Reoxidation of the catalyst is found to be important for the product release at the end of the reaction.