Experimental and ab initio study of a new D 1Deltag state of the C3 radical

We report here the first observation of the D (1)Delta(g) state of the C(3) radical, which provides the first comprehensively analyzed example of the dynamic Renner-Teller splitting in Delta symmetry. Two color double resonance spectroscopy via the A (1)Pi(u) state was employed to experimentally probe an extensive range of vibronic levels in this D (1)Delta(g) state, covering all three modes of vibration of C(3). The analysis was supported by ab initio potential energy surface calculations on the C(3) radical to outline the lowest eight singlet electronic states. Two methods were used to analyze the Renner-Teller effect. The first method is an empirical Hamiltonian based on normal modes, using harmonic oscillator functions as a basis, with Renner-Teller and other terms added as required, which allows conventional vibrational parameters to be determined. The second is a much larger program that uses the exact kinetic energy operator for a triatomic molecule to calculate vibronic energy levels directly from the Renner-Teller pair of potential energy surfaces. Both methods give a good fit to the experimental results, with only a small adjustment to the ab initio surfaces required for the latter. One of the overall conclusions is that the Renner-Teller effect is rather smaller in the D (1)Delta(g) state than in the A (1)Pi(u) state.     

Electronic and transport properties of silicene-based ammonia nanosensors: an ab initio study

Structural Chemistry - Using density functional theory (DFT) and non-equilibrium Green’s function (NEGF) formalism, the electronic and transport properties of ammonia (NH3) molecule adsorbed...     

Structure and properties of a model of deoxyheme,an ab initio SCF calculation

Ab initio SCF calculations have been used to study the structure and the electronic properties of four- and five-coordinate Fe(II) porphyrins. The following systems have been considered: FeP (P = porphine dianion) (S = 1 and S = 2) and Fe(NH₂)₄ (S = 1) as four-coordinate systems. FePNH₃, Fe(NH₂)₄NH₃ and Fe(NH₂)₄1m as models of the deoxyheme (S = 2). Fe(NH₂)₄SH (S = 2) as a model of the reduced cytochrome P450. The basis sets used are either of the split-valence type or of double-zeta quality. The ground-state electronic configurations have been assigned. The potential energy curve of FePNH₃, as a function of the out-of-plane displacement of the iron atom, has a minimum for a displacement of 0.32 Å. a value significantly smaller than the accepted value of 0.6 Å in human deoxyhemoglobin. The out-of-plane displacement is larger, by ≈ 0.2 Å, when a mercaptide ligand replaces the ammonia or imidazole ligand. The electric field gradient tensor, the quadrupole splitting and the asymmetry parameter have been calculated and compared with the experimental values derived from the ⁵⁷Fe Mössbauer spectra.     

Development of an ab initio emulsion atom transfer radical polymerization: from microemulsion to emulsion

Atom transfer radical polymerization (ATRP) has been successfully extended to an ab initio emulsion system using a "two-step" procedure, in which the final emulsion polymerization system was formed by adding monomer to an ongoing microemulsion ATRP. The newly developed AGET (activators generated by electron transfer) initiation technique was employed in the first stage of this ab initio ATRP. It allows using oxidatively stable Cu(II) species that is reduced in situ by ascorbic acid. The surfactant concentration in the final emulsion system was efficiently decreased to approximately 2 wt % (approximately 10 wt % vs monomer) by decreasing the catalyst concentration and changing the ratio of the monomer added at the microemulsion stage to the monomer added during the second stage. This two-step procedure avoids the necessity of transporting catalysts through the aqueous media during polymerization, resulting in a controlled emulsion polymerization, as evidenced by a linear first-order kinetic plot and formation of a polymer with a relatively narrow molecular weight distribution (Mw/Mn = 1.2-1.4). The polymerization typically reached 70-90% monomer conversion in 5-6 h. The resulting polymer had high chain-end functionality and was successfully chain extended to form in situ block copolymers by adding the second monomer to an ongoing emulsion polymerization. The stable latex from the ab initio emulsion ATRP had a particle size approximately 120 +/- 10 nm.     

Size-expanded DNA bases: an ab initio study of their structural and electronic properties

The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order M?ller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have also nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.     

Pseudorotation motion in tetrahydrofuran: an ab initio study

The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.     

Electronic structure of the cysteine thiyl radical: a DFT and correlated ab initio study

The electronic structure and the unusual EPR parameters of sulfur-centered alkyl thiyl radical from cysteine are investigated by density functional theory (DFT) and correlated ab initio calculations. Three geometry-optimized, staggered conformations of the radical are found that lie within 630 cm(-1) in energy. The EPR g-values are sensitive to the energy difference between the nearly-degenerate singly occupied orbital and one of the lone-pair orbitals (excitation energies of 1732, 1083, and 3429 cm(-1) from Multireference Configuration Interaction calculations for the structures corresponding to the three minima), both of which are almost pure sulfur 3p orbitals. Because of the near degeneracy, the second order correction to the g tensor, which is widely used to analyze g-values of paramagnetic systems, is insufficient to obtain accurate g-values of the cysteine thiyl radical. Instead, an expression for the g tensor must be used in which third order corrections are taken into account. The near-degeneracy can be affected to roughly equal extents by changes in the structure of the radical and by hydrogen bonds to the sulfur. The magnitude of the hyperfine coupling constants for the beta protons of the cysteine thiyl radical is found to depend on the structure of the radical. On the basis of a detailed comparison between experimental and calculated g-values and hyperfine coupling constants an attempt is made to identify the structure of thiyl radicals and the number of hydrogen bonds to the sulfur.     

Adsorption of RDX and TATP on IRMOF-1: an ab initio study

The adsorption of 1,3,5-trinitro-s-triazine (RDX) and triacetone triperoxide (TATP) on representative fragments of metal organic framework (IRMOF-1) was studied at the B3LYP/6-31G(d) level of theory. For examined adsorbates several possible adsorption positions toward the IRMOF-1 fragments were found. The adsorption strength of the adsorbate on IRMOF-1 is largely affected by the geometry of the active site of IRMOF-1 which controls the orientation of the target molecule with respect to the IRMOF-1 fragment. The calculations show that the adsorption on these fragments occurs due to the formation of hydrogen bonds between the molecular C–H groups and the oxygen atoms of IRMOF-1. The RDX and TATP molecules are the most strongly adsorbed on the linker fragment of IRMOF-1. This type of adsorption results in the polarization of RDX and TATP on the IRMOF-1 fragments. The interaction energy of two most stable RDX-, and TATP-IRMOF-1 adsorption systems are ?9.8 and ?12.8 kcal/mol, respectively. It can be concluded that the 1,4-benzenedicarboxylate site of IRMOF-1 shows the stronger molecular adsorption of RDX and TATP than the site containing [Zn₄O(CO₂)₆] and also it is characterized by higher reactivity than the other considered sites. The binding of studied explosive molecules to IRMOF-1 consists of interplay between attractive interactions between the target molecule and MOF as well as the shielding by the IRMOF-1 fragment induced by the molecular adsorption. The relative importance of these effects depends on the chemical nature, the size, and the shape of the molecule and MOF. Small-size molecules require smaller space for the adsorption and also they are less shielded by the sizeable adsorbent. So they interact better when adsorbed on larger IRMOF-1 fragment. On the other side, larger molecules show higher adsorption strength with small fragments of IRMOF-1.     

Solvent-dependent stereoselectivity in a Still-Wittig rearrangement: an experimental and ab initio study

[see reaction]. The Still-Wittig rearrangement gave opposite selectivities for (Z:E)-alkenes in THF (3:1) vs toluene (1:3) in the synthesis of serine-proline dipeptide amide isosteres. Four transition states leading to (Z)-and (E)-alkenes with THF and without (representing toluene) were identified by ab initio calculations at the 3-21G* level. The calculated (Z:E)-ratios with THF (4.7:1) and without THF (1:3.2) suggested that the transition state geometries and energies were well-represented by the calculations.     

Hydrogen physisorption on the organic linker in metal organic frameworks: ab initio computational study

Research for materials offering efficient hydrogen storage and transport has recently received increased attention. Metal organic frameworks (MOFs) provide one promising group of materials where several recent advances were reported in this direction. In this computational study ab initio methods are employed to study the physisorption of hydrogen on conjugated systems. These systems are used as models for the organic linker within MOFs. Here, we focus on the adsorption sites related to the organic linker with special attention to the edge site, which was only recently reported to exist as the weakest adsorbing site in MOFs. We also investigate chemically modified models of the organic connector that result in enforcing this adsorption site. This may be crucial for improving the uptake properties of these materials to the goal defined by DOE for efficient hydrogen transport materials.     

The box model as a basis for an ab initio procedure

The results of the procedure developed in [1] are reported for the hydrogen molecule. It appears that the phenomenon of bonding can at least be qualitatively reproduced.

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Die Rechnungen sind im Deutschen Rechenzentrum, Darmstadt, und im Rechenzentrum der Bayerischen Akademie der Wissenschaften, München, durchgeführt worden. Die finanziellen Mittel stammten aus dem Sonderforschungsbereich Theoretische Chemie.     

Ozone-water 1:1 complexes O3-H2O: an ab initio study

Ab initio MO calculations have been carried out for the ozone-water 1:1 complexes in order to elucidate the structures and electronic state of the complexes. The QCISD calculations indicated that three structures are obtained as stable forms of O(3)-H(2)O. The most stable structure of O(3)-H(2)O has C(s) symmetry where the central oxygen of O(3) and all atoms of H(2)O are located on the molecular C(s) plane. The dipole of H(2)O orients toward the central oxygen atom of O(3) (i.e., dipole orientation form). The other two forms are cis and trans forms of O(3)-H(2)O where all atoms are located on the molecular plane, and a hydrogen of H(2)O binds to one of the terminal oxygen atoms of O(3) by a hydrogen bond. The binding energies of O(3) to H(2)O for dipole, cis, and trans forms are calculated to be 2.39, 2.27, and 2.30 kcal/mol, respectively, at the QCISD(T)/6-311++G(3df,3pd)//QCISD/6-311++G((d,p) level. The dipole orientation form is more stable in energy than the cis and trans forms. Rotational constants for the dipole orientation form are calculated to be A = 11.897, B = 4.177, and C = 3.318 GHz which are in good agreement with the experimental values (A = 11.961, B = 4.174, and C = 3.265 GHz). The electronic states of O(3)-H(2)O were discussed on the basis of theoretical results.     

Organic carbonates: experiment and ab initio calculations for prediction of thermochemical properties

This work has been undertaken in order to obtain data on thermodynamic properties of organic carbonates and to revise the group-additivity values necessary for predicting their standard enthalpies of formation and enthalpies of vaporization. The standard molar enthalpies of formation of dibenzyl carbonate, tert-butyl phenyl carbonate, and diphenyl carbonate were measured using combustion calorimetry. Molar enthalpies of vaporization of these compounds were obtained from the temperature dependence of the vapor pressure measured by the transpiration method. Molar enthalpy of sublimation of diphenyl carbonate was measured in the same way. Ab initio calculations of molar enthalpies of formation of organic carbonates have been performed using the G3MP2 method, and results are in excellent agreement with the available experiment. Then the group-contribution method has been developed to predict values of the enthalpies of formation and enthalpies of vaporization of organic carbonates.     

Product branching ratios in photodissociation of phenyl radical: a theoretical ab initio/Rice-Ramsperger-Kassel-Marcus study

Ab initio CCSD(T)/CBS//B3LYP/6-311G** calculations of the potential energy surface for possible dissociation channels of the phenyl radical are combined with microcanonical Rice-Ramsperger-Kassel-Marcus calculations of reaction rate constants in order to predict statistical product branching ratios in photodissociation of c-C(6)H(5) at various wavelengths. The results indicate that at 248 nm the photodissociation process is dominated by the production of ortho-benzyne via direct elimination of a hydrogen atom from the phenyl radical. At 193 nm, the statistical branching ratios are computed to be 63.4%, 21.1%, and 14.4% for the o-C(6)H(4) + H, l-C(6)H(4) ((Z)-hexa-3-ene-1,5-diyne) + H, and n-C(4)H(3) + C(2)H(2) products, respectively, in a contradiction with recent experimental measurements, which showed C(4)H(3) + C(2)H(2) as the major product. Although two lower energy pathways to the i-C(4)H(3) + C(2)H(2) products are identified, they appeared to be kinetically unfavorable and the computed statistical branching ratio of i-C(4)H(3) + C(2)H(2) does not exceed 1%. To explain the disagreement with experiment, we optimized conical intersections between the ground and the first excited electronic states of C(6)H(5) and, based on their structures and energies, suggested the following photodissociation mechanism at 193 nm: c-C(6)H(5) 1 → absorption of a photon → electronically excited 1 → internal conversion to the lowest excited state → conversion to the ground electronic state via conical intersections at CI-2 or CI-3 → non-statistical decay of the vibrationally excited radical favoring the formation of the n-C(4)H(3) + C(2)H(2) products. This scenario can be attained if the intramolecular vibrational redistribution in the CI-2 or CI-3 structures in the ground electronic state is slower than their dissociation to n-C(4)H(3) + C(2)H(2) driven by the dynamical preference.     

Resonance and aromaticity: an ab initio valence bond approach

Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randi?'s conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.     

Interactions of Li, Ca, and Al with aromatic carbon materials: an ab initio study

The interactions of benzene (C6H6), naphthalene (C10H8), and perinaphthene (C13H9) with metal atoms (Li, Ca, and Al) were studied using second-order M?ller-Plesset perturbation theory. By analyzing the frontier molecular orbitals, geometric structures, binding energies, and charge transfers, it was found that these metal atoms can bond strongly with C13H9, but can only bond weakly with C6H6 and C10H8. The bonding nature between a metal atom and C13H9 at their ground state depends significantly on the valence orbital of the metal atom and the pi-bonding distribution of the aromatic hydrocarbons. The spindly shaped 3p valence orbital of an Al atom results in the deviation of the adsorption site to the edge of C13H9, whereas the ball-shaped 2s/4s valence orbitals of a Li and a Ca atom facilitate their overlap with the second lowest unoccupied molecular orbital of C13H9. Further, Hartree-Fock and density-functional theory methods were demonstrated generally to be unreliable in describing the interactions of metal atoms with these pi systems.     

Electron attachment in ice-HCl clusters: an ab initio study

Experimental work has shown that small amounts of HCl strongly enhance electron capture in ice films. The purpose of the present study was to investigate the effect of adsorbed HCl on the interaction of electrons with small clusters of water. Studies were made with clusters of 6 and 12 water molecules with various geometries both with and without one HCl attached. A number of distinct HCl coordination motifs were examined. All of the neutral structures with HCl exhibited zero thresholds for electron attachment and formed dipole bound anionic states (DBS). The relaxation processes for these "initial DBS" depended on the number of H(2)O (n) and on the number and type of H-bonds to the HCl (x). The initial DBS of systems with only O-H...Cl H-binding underwent dissociative electron attachment (DEA), forming H atoms. Relaxation for systems with ClH...OH(2) bonds was more complex. For the two layer n = 12 systems with x = 2 or 3 the HCl proton moved to the nearest oxygen to form H(3)O(+). Then rearrangement of the proton network occurred, and the Cl(-) became solvated by three HO-H...Cl(-) bonds. The presence of Cl(-) and H(3)O(+) increases the dipole moment and the electron binding energy (EBE) of the network. Further stabilization is achieved by decay into deeper DBS electron traps and/or by reaction of the excess electron with H(3)O(+) to form H(*) atoms. The HCl(H(2)O)(6) clusters with a single Cl-H...OH(2) bond behaved differently. They increased their stability by becoming more linear. This raised the dipole moment and the EBE therefore increased, reducing the total energy. None of these species showed any signs of increasing the number of H-bonds to Cl. The implication of these observations for the interpretation of the results of the experiments with 0.2 monolayer of HCl on 5 monolayer of H(2)O at 20 K, and on the possible role of cosmic ray-induced ionization in polar stratospheric clouds in ozone depletion is discussed.     

Copolymers of carbon dioxide and nitrogen: an AM1 and ab initio computational study

Extending work by various groups on possible dimers, trimers, etc. of dinitrogen and of carbon dioxide, the authors have studied analogous copolymers of N₂ and CO₂ computationally. Twelve cyclic structures were examined with the AM1, HF/3-21G, HF/6-31G* and MP2(FC)/6-31G* methods, and the acyclic “monomer” to “tetramer” HO(C(O)O–N= N–)_nH, n=1–4, were studied at the AM1 and HF/3-21G levels; the cyclic species included 2-oxa-3,4-diazacyclobut-3-ene-1-one, 2-oxa-3,4,5,6-tetraazacyclohexa-3,5-diene-1-one, and various aza/oxa bicyclo[2.2.0] and bicyclo[2.2.2] systems. For the cyclic species, it was concluded that only the MP2(FC)/6-31G* results, which differ considerably from those at the other three levels, are likely to be reliable. These MP2 calculations indicate that only seven of the 12 cyclic structures studied are stationary points (one is a transition structure), and none of them is kinetically stable at room temperature. Although some have high energy densities (ca. 7–10 kJ g⁻¹), their expected low kinetic stabilities seems to make this of little practical value. The acyclic “copolymers” were all relative minima at the AM1 and HF/3-21G levels; unlike the cyclic species, their kinetic stabilities were not investigated directly by comparing the energies of reactants and decomposition transition states. The energy density of the infinite acyclic polymer was found by extrapolation to be 5.1 (AM1) or 5.6 (3-21G) kJ g⁻¹. The calculated vibrational spectra of the MP2 stationary points and of the acyclic molecules gave some indication of instability by the presence of low-frequency modes leading in the limit to decomposition.     

Conformational stability of a model macrocycle tetraamide: an ab initio study

Ab initio calculations are carried out to investigate the conformational stability of a model macrocyle tetraamide. The four amide groups in the selected model are present in the sequence: -(O=CNH)-Ph-(NHC=O)-CH=CH-(O=CNH)-Ph-(NHC=O)-CH=CH-. In this sequence, two phenyl rings and two ethene groups act as bridges between the amide units. Each amide motif bonds to a phenyl ring through its amide nitrogen and to an ethene group through its amide carbon. Four clearly distinct minimum-energy conformations are found upon full geometry optimization using the B3LYP/6-31+G(d) method. Frequency calculations using the same method confirm that the four conformations are indeed minima in the macrocycle potential energy surface. Relative to the most stable conformer, the other conformations are higher in energy by 0.86, 2.09, and 9.17 kcal/mol, respectively, at the MP2/6-31+G(d,p) level. The stability of the macrocycle conformations is correlated primarily to the existence and strength of intramolecular N-H...O=C hydrogen bonds. Additional stability to the conformations is found to come from weak Ph-H...O=C hydrogen bonding between a carbonyl oxygen and a hydrogen atom of a phenyl group. Solvent effects play an important role in the relative energies of the various conformations, as indicated by the simple SCRF = dipole model calculations for the case of aqueous solution.     

Enthalpy of formation of the cyclopentadienyl radical: photoacoustic calorimetry and ab initio studies

The gas-phase C-H bond dissociation enthalpy (BDE) in 1,3-cyclopentadiene has been determined by time-resolved photoacoustic calorimetry (TR-PAC) as 358 +/- 7 kJ mol(-1). Theoretical results from ab initio complete basis-set approaches, including the composite CBS-Q and CBS-QB3 procedures, and basis-set extrapolated coupled-cluster calculations (CCSD(T)) are reported. The CCSD(T) prediction for the C-H BDE of 1,3-cyclopentadiene (353.3 kJ mol(-1)) is in good agreement with the TR-PAC result. On the basis of the experimental and the theoretical values obtained, we recommend 355 +/- 8 kJ mol(-1) for the C-H BDE of 1,3-cyclopentadiene and 271 +/- 8 kJ mol(-1) for the enthalpy of formation of cyclopentadienyl radical.