A zinc-containing porphyrin aluminum MOF in sorption of diethyl sulfide vapor: mechanistic experimental and computational study.

We report a mechanistic study of the interactions in the sorption of volatile organic sulfur compound (VOSC) diethyl sulfide (DES) by zinc porphyrin aluminum MOF (actAl-MOF-TCPPZn) compound 3. First, interactions were studied under dynamic conditions with the vapor of DES in flowing air, using in situ time-dependent ATR-FTIR spectroscopy in a controlled atmosphere with a new facile spectroscopic mini-chamber. The first binding site includes µ(O-H) and COO- groups as detected by characteristic peak shifts. Control experiments with a model compound, which lacks porosity and these groups, show no peak shifts. An additional insight was obtained by DFT computations using small clusters. The kinetics of sorption of DES by compound 3 is of the Langmuir adsorption model and pseudo-first order with rate constant robs = 0.442 ± 0.056 min-1. Sorption of DES under static conditions in saturated vapor results in stoichiometric adsorption complex [Al-MOF-TCPPZn]1(DES)4 characterized by spectroscopic, structural and gravimetric methods; the adsorbed amount is very high (381 mg g-1 sorbent). The repetitive sorption and desorption of DES are conducted, with facile regeneration. Finally, the mechanistic details were determined by Raman and photoluminescence (PL) spectroscopy using a confocal Raman microscope. Photoexcitation of compound 3 at 405 nm into the Soret band of the metalloporphyrin linker shows the characteristic PL peaks of Q-bands: the purely electronic Q(0-0) and first vibronic Q(0-1) bands. Upon interaction with DES, preferential quenching of PL from the Q(0-0) band occurs with a significant increase of the signal of the vibronic Q(0-1) band, reflecting bonding to the metalloporphyrin ring. Compound 3 is of interest to mechanistic studies of VOSCs, their removal from air, and optical chemo-sensing.

DFT Surface Infers Ten-Vertex Cationic Carboranes from the Corresponding Neutral closo Ten-Vertex Family: The Computed Background Confirming Their Experimental Availability.

Modern computational protocols based on the density functional theory (DFT) infer that polyhedral closo ten-vertex carboranes are key starting stationary states in obtaining ten-vertex cationic carboranes. The rearrangement of the bicapped square polyhedra into decaborane-like shapes with open hexagons in boat conformations is caused by attacks of N-heterocyclic carbenes (NHCs) on the closo motifs. Single-point computations on the stationary points found during computational examinations of the reaction pathways have clearly shown that taking the "experimental" NHCs into account requires the use of dispersion correction. Further examination has revealed that for the purposes of the description of reaction pathways in their entirety, i.e., together with all transition states and intermediates, a simplified model of NHCs is sufficient. Many of such transition states resemble in their shapes those that dictate Z-rearrangement among various isomers of closo ten-vertex carboranes. Computational results are in very good agreement with the experimental findings obtained earlier.

Exploring the Reaction Mechanism of C-H Oxidation by Copper-Salen Complexes.

The mechanism of C-H oxidation of propylene (C3H6) and 1-phenyl-1-pentyne (C3H7-C≡C-Ph) by HOOR (R═Me, tBu) and 3O2 by a copper-salen complex was explored by computations. The most noteworthy step is the complexation of two Cu salens to the peroxide to form either the LCuOH/LCuOR pair or an OH-bridged complex LCu(µ-OH)CuL plus OR. The latter pathway involves an avoided crossing of two triplet electronic states. The LCuOH complex can abstract a hydrogen atom from C3H6 and the C3H5 radical plus 3O2 forms the complex LCuOOC3H5. Migration of a hydrogen to the proximal oxygen atom reforms LCuOH and acrolein HC(O)CH═CH2.

Evaluation of packing single and multiple atoms and molecules in the porous organic cage CC3-R.

The absorption of multiple atoms and molecules, including Kr, Xe, CH4, CO2, C2H2, H2O, and SF6, within CC3-R, a Porous Organic Cage (POC), was calculated and analyzed. The CC3-R molecule has one central cavity and four window sites. Most adsorbents were modeled with either one unit in the central cavity, four units in the window sites, or with five units in both sites. For Xe, the most favorable site was the central one. The CO2 molecule binds about 3 kcal mol-1 in free energy more strongly than CH4 in the central cavity of CC3-R at 300 K which may be enough to allow useful discrimination. Four C2H2 units and four CO2 units are calculated to bind similarly inside CC3-R (ΔH(298 K) = -8.6 and -7.7 kcal mol-1 per unit, respectively). Since H2O is smaller, more waters can easily fit inside. For twelve water molecules, the binding enthalpy per water is ΔH(298 K) = -16.4 kcal mol-1. For comparison, the binding enthalpy of (H2O)12 at the same level of theory (B3LYP/6-31G(d,p)-D3BJ//M06-2X/6-31G(d)) is predicted to be -12.3 kcal mol-1 per water. Finally, the dimerization of CC3-R and the association of CC3-R with CC3-S was studied as well as 3 to 9 iodine atoms enclosed in CC3-R.

Theoretical Study of Methane Storage in Cu24(m-BDC)24.

Calculations on the Cu24(m-BDC)24 (m-BDC = 1,3-benzenedicarboxylate) polyoxometalate (POM) cage with 0, 12, 24, and 40 methane molecules inside were made using the M06 exchange/correlation functional. During filling of the cage with 40 CH4 molecules, the 12 strongest binding CH4 molecules are those to the coordination unsaturated sites (CUS) to the inwardly directed Cu(+2) centers via agostic interactions. The next 12 CH4 molecules are less tightly bound followed by the next 16 CH4 molecules with average binding energies of 8.27, 7.88, and 7.36 kcal/mol per CH4, respectively. A section of the Cu24(m-BDC)24 cage was taken with the formula Cu4(m-BDC)(BC)6 (BC = benezenecarboxylate) in order to estimate zero-point, thermal, and entropy corrections of the larger cage. Estimating free energies at 1 bar, the Cu24(m-BDC)24 POM is predicted to lose 16, 12, and 12 CH4 molecules at 67, 123, and 171 °C, respectively. The 40CH4@Cu24(m-BDC)24 cage, which is isostructural to the main cavity of HKUST-1 with 40 CH4 molecules inside, is predicted to have a loading of 224 cm3(STP) cm-3 at 1 bar.

Unusual Cage Rearrangements in 10-Vertex nido-5,6-Dicarbaborane Derivatives: An Interplay between Theory and Experiment.

The reaction between selected X-nido-5,6-C2B8H11 compounds (where X = Cl, Br, I) and "Proton Sponge" [PS; 1,8-bis(dimethylamino)naphthalene], followed by acidification, results in extensive rearrangement of all cage vertices. Specifically, deprotonation of 7-X-5,6-C2B8H11 compounds with one equivalent of PS in hexane or CH2Cl2 at ambient temperature led to a 7 → 10 halogen rearrangement, forming a series of PSH+[10-X-5,6-C2B8H10]- salts. Reprotonation using concentrated H2SO4 in CH2Cl2 generates a series of neutral carbaboranes 10-X-5,6-C2B8H11, with the overall 7 → 10 conversion being 75%, 95%, and 100% for X = Cl, Br, and I, respectively. Under similar conditions, 4-Cl-5,6-C2B8H11 gave ∼66% conversion to 3-Cl-5,6-C2B8H11. Since these rearrangements could not be rationalized using the B-vertex swing mechanism, new cage rearrangement mechanisms, which are substantiated using DFT calculations, have been proposed. Experimental 11B NMR chemical shifts are well reproduced by the computations; as expected δ(11B) for B(10) atoms in derivatives with X = Br and I are heavily affected by spin-orbit coupling.

The behavior of a paramagnetic system in electric and magnetic fields as exemplified by revisiting Li@B10H14.

The electric and magnetic properties of the Li@B10H14 complex, considered as a novel inorganic electride-type system with potential for second-order non-linear optical (NLO) applications, have already been studied. However, the reported C2v structure is not the global energy minimum and therefore its electronic and magnetic properties need to be revisited. Moreover, by applying more accurate computational protocols (ROHF-CCSD/CCSD(T) and larger basis sets) we show that the model chemistry used earlier (UMP2/6-31+G(d)) is not sufficient for reliable description of the NLO responses of this open-shell doublet complex. The global minimum based on the Cs symmetry is significantly (by ca. 25 kcal mol-1) more stable than the C2v structure and it should be viewed as a system with moderate NLO responses. An excess of unpaired electron density is also responsible for the contact and pseudo-contact contributions to the magnetic properties, which was not considered in the earlier work.

Density Functional Study of Neutral and Charged Silver Clusters Agn with n = 2-22. Evolution of Properties and Structure.

Geometries and electronic properties of neutral Agn, cationic Agn+, and anionic Agn- silver clusters with n = 2-22 were investigated by density functional theory (DFT) with M06 functional. For neutral clusters, transition from planar to "empty cage" structure occurs at n = 7, "empty cage" to "cage with one Ag atom" at n = 18, and to "cage with two Ag atoms" at n = 22. For lowest-energy Agn clusters, Ag8 and Ag18 show lowest polarizability due to closed-shell valence electron configurations 1S2/1P6 and 1S2/1P6/1D10. High stability of Ag8 is manifested in small dissociation energies of Ag9 to Ag8 plus Ag1 and Ag10 cluster to Ag8 plus Ag2. Cluster Ag20 with configuration 1S2/1P6/1D10/2S2 is stable due to low dissociation energy of Ag21 to Ag1 and Ag22 to Ag2. Cationic clusters with even n namely Ag10+ (9 valence electrons), Ag16+ (15 valence electrons), and Ag22+ (21 valence electrons) dissociate to Ag1 and closed-shell Ag9+ (1S2/1P6), Ag15+ (1S2/1D10/2S2) and Ag21+ (1S2/1P6/1D10/2S2). For odd n, Ag11+ and Ag17+ dissociate to Ag2 and closed-shell Ag9+ and Ag15+. For anionic clusters Agn-, cohesion energy Ecoh and binding energy (BE) show maxima at n = 7 and n = 17 due to stable Ag7- and Ag17- clusters. Small Agn- clusters (n = 4-11) with even n (except n = 8) have lower dissociation energy for loss of Ag1 while those with odd n have lower dissociation energy for loss of Ag2. For n = 12-22, all clusters have lower dissociation energy for loss of Ag1.

Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study.

An intriguing stepwise diradical mechanism of the dimerization of the reactive intermediate (thiocarbonyl S-methanide) appearing in the reaction of phenyl selenophen-2-yl thioketone with diazomethane was studied by means of computational methods. The preferred formation of the unusual macroheterocycle, competitive with the 1,3-ring closure leading to a thiirane and the head-to-head dimerization yielding a 1,4-dithiane derivative, respectively, was explained based on the analysis of the structure of the favored conformer of the intermediate, delocalized diradical species. The influence of selenium as a 'heavy atom' for stabilization of this intermediate has been emphasized.

Saturn Systems.

Several ring systems (Saturn systems) have been studied using DFT methods that include dispersion effects. Comparison with X-ray structures are made with three systems, and the agreement is quite good. Binding enthalpies and binding free energies in dichloromethane and toluene have been computed. The effect of an encapsulated lithium cation is accessed by comparing C60 @(C6 H4 )10 and [Li@C60 @(C6 H4 )10 ](+). The [Li@C60 ](+) cation is a much better acceptor than C60 which leads to greater donor-acceptor interactions and larger charge transfer from the ring to [Li@C60 ](+).

A New Nitrogenase Mechanism Using a CFe8S9 Model: Does H2 Elimination Activate the Complex to N2 Addition to the Central Carbon Atom?

A truncated model of the FeMo cofactor is used to explore a new mechanism for the conversion of N2 to NH3 by the nitrogenase enzyme. After four initial protonation/reduction steps, the H4CFe8S9 cluster has two hydrogen atoms attached to sulfur, one hydrogen bridging two iron centers and one hydrogen bonded to carbon. The loss of the CH and FeHFe hydrogens as molecular hydrogen activates the cluster to addition of N2 to the carbon center. This unique step takes place at a nearly planar four-coordinate carbon center and leads to an intermediate with a significantly weakened N-N bond. A hydrogen attached to a sulfur atom is then transferred to the distal nitrogen atom. Additional prontonation/reduction steps are modeled by adding a hydrogen atom to sulfur and locating the transition states for transfer to nitrogen. The first NH3 is lost in a thermal neutral step, while the second step is endothermic. The loss of H2 activates the complex by reducing the barrier for N2 addition by 3.5 kcal/mol. Since this is the most difficult step in the mechanism, reducing the barrier for this step justifies the "extra expense" of H2 production.

Computational Study of Reduction Potentials of Th4+ Compounds and Hydrolysis of ThO2(H2O)n, n = 1, 2, 4.

The stability of Th4+ to reduction in water is studied by DFT methods. The standard reduction potential (SRP) of homoleptic complexes including Th(H2O)94+, Th(H2O)104+, Th(NO3)4, Th(NO2)62-, Th(NO3)62-, Th(COT)2, Th(acac)4, ThCp4, ThF4, and ThCl4 have been investigated. The values vary widely (from -3.50 V for Th(OH)4 to -0.62 V for Th(NO3)4 depending on whether the ligands are redox active (noninnocent) or not. Several additional topics of thorium chemistry are explored, including the hydrolysis mechanism of ThO2(H2O)n, n = 1, 2, 4, and the solution phase nonzero dipole moment of ThCp4. Dinuclear complexes are also characterized, including Th2O4, Th2O2(OH)4, Th2O2(H2O)8, Th2(OH)8(H2O)4, and Th2(OH)2(NO3)6(H2O)4 and condensed thorium complexes as [Th4(OH)6(H2O)12]10+ and [Th6(OH)14(H2O)12]10+. For the Th2(OH)2(NO3)6(H2O)4 dinuclear complex, the first SRP is -0.82 V and the second is 1.59 V. The first SRP corresponds to the reduction of the ligand NO3-, and the second SRP corresponds to dissociative electron transfer to the NO32- ligand. The calculated formation constant of Th(EDTA)(H2O)4 is in reasonable agreement with experiment. The different stereochemistries of the bidentate ligands NO2-, NO3-, and acetylacetonate (acac) around the thorium center have very similar stabilities.

Computational examination of the mechanism of alkene epoxidation catalyzed by gallium(III) complexes with N-donor ligands.

The ability of gallium(III) complexes to catalyze the epoxidation of alkenes by peracetic acid has been examined with density functional theory calculations. According to the calculations, the chloride anions of the precatalyst [Ga(phen)2Cl2](+) (phen = 1,10-phenanthroline) can be displaced by either acetic or peracetic acid through dissociative ligand exchange pathways; both acetic and peracetic acid deprotonate upon binding to the formally tricationic metal center. Because of the high basicity of peracetate relative to that of chloride, only the acetate for chloride exchange occurs spontaneously, providing a rationale for the preponderance of gallium acetate adducts observed in the reaction mixtures. With respect to the mechanism of olefin epoxidation, the computational results suggest that the peracetic acid is most efficiently activated for redox activity when it binds to the metal center in a κ(2) fashion, with the carbonyl oxygen atom serving as the second point of attachment. The phen ligands' coordination to the gallium is essential for the catalysis, and the lowest energy pathways for alkene oxidation proceed through hexacoordinate Ga(III) species with four Ga-N bonds. A natural bond order analysis confirms the electrophilic nature of the metal-containing oxidant.

Combined ab initio molecular dynamics and experimental studies of carbon atom addition to benzene.

Car-Parrinello molecular dynamics was used to explore the reactions between triplet and singlet carbon atoms with benzene. The computations reveal that, in the singlet C atom reaction, products are very exothermic where nearly every collision yields a product that is determined by the initial encounter geometry. The singlet C atom reaction does not follow the minimum energy path because the bimolecular reaction is controlled by dynamics (i.e., initial orientation of encounter). On the other hand, in a 10 K solid Ar matrix, ground state C((3)P) atoms do tend to follow RRKM kinetics. Thus, ab initio molecular dynamics (AIMD) results indicate that a significant fraction of C-H insertion occurs to form phenylcarbene whereas, in marked contrast to previous theoretical and experimental conclusions, the Ar matrix isolation studies indicate a large fraction of direct cycloheptatetraene formation, without the intermediacy of phenylcarbene. The AIMD calculations are more consistent with vaporized carbon atom experiments where labeling studies indicate the initial formation of phenylcarbene. This underlines that the availability of thermodynamic sinks can completely alter the observed reaction dynamics.

Computational study of the initial stage of diborane pyrolysis.

The rate constants for the association of two boranes to form diborane are investigated using several methods. The most sophisticated method is the variable reaction coordinate-variational transition state theory (VRC-VTST) which has been developed to handle reactions with no enthalpic barriers. The calculated rate constant of 8.2 × 10(-11) cm(3)·molecule(-1)·s(-1) at 545 K is in good agreement with experiment. The rate constant was also computed using conventional VTST with the G4 composite method. Two variations of the multistep mechanisms for diborane pyrolysis are presented. One is initiated by the step B2H6 ⇄ 2 BH3 while the other begins with 2 B2H6 ⇄ B3H9 + BH3 as the initial elementary step. Both variations are 3/2 order in diborane and have the same activation energy (G4, 28.65 kcal/mol at 420 K). In contrast, the traditional mechanism involving a B3H9 intermediate with C3v symmetry has a higher activation energy (33.37 kcal/mol). The two variations involve a C2-symmetry penta-coordinate B3H9 structure that, while an electronic minimum, is not a stationary point on the free energy path between B2H6 + BH3 → B3H7 + H2. While the calculated activation barrier is higher than the recently determined experimental barrier, the variation in reported values is large (22.0-29.0 kcal/mol). We discuss possible sources of disagreement between experiment and theory.

Moving atoms and small molecules out of open containers.

Density functional theory with the M05-2X exchange/correlation functional is used to study the barriers for expulsion of atoms and small molecules (N2, CO, H2, Ar, Kr, Xe, H2O) out of open fullerenes (I20) and related molecular containers (C40H20, [5]beltene, cucurbit[5]uril). The reactions are examples where dispersion plays a critical role in determining the barrier heights. Calculations are compared with experimental kinetic data for N2@I20, CO@I20, and Xe@cucurbit[5]uril (Xe@CB[5]). Comparing the four molecular containers, the activation barriers for escape of an atom or small molecule correlate with the binding energies. A new open-fullerene model container C40H20 (C40) was constructed from C60 with a constriction at both ends formed by five methylene groups around the rim. The activation barriers for escape of N2 and CO from the model container are similar to those from the I20 open-cage fullerene. In the case of H2O@C40, charge analysis reveals an interesting charge transfer at the transition state as the escaping guest is "squeezed" out of the host container.

Evaluating the role of triborane(7) as catalyst in the pyrolysis of tetraborane(10).

The initial steps in the B4H10 pyrolysis mechanism have been elucidated. The mechanism can be divided into three stages: initial formation of B4H8, production of volatile boranes with B3H7 acting as a catalyst, and formation of nonvolatile products. The first step is B4H10 decomposition to either B4H8/H2 or B3H7/BH3 where the free energy barrier for the first pathway is 5.6 kcal/mol higher (G4, 333 K) than the second pathway when transition state theory (TST) is used. When variation transition state theory (VTST) is used for formation of B3H7/BH3, the two pathways become very similar in free energy with the B4H8/H2 pathway becoming favored at G4 by 1.0 kcal/mol at 333 K (33.1 versus 34.1 kcal/mol). The experimental activation energy for B4H10 pyrolysis is about 10 kcal/mol lower than the calculated barrier for B4H10 → B4H8 + H2, which indicates that this reaction is not the rate-determining step. We suggest that the rate-determining step is B4H10 + B3H7 → B4H8 + H2 + B3H7 where B3H7 acts as a catalyst. The role of reactive boron hydrides such as B3H7 and B4H8 as catalysts in the build-up of larger boron hydrides may be more common than that previously considered.

Interaction of a Porphyrin Aluminum Metal-Organic Framework with Volatile Organic Sulfur Compound Diethyl Sulfide Studied via In Situ and Ex Situ Experiments and DFT Computations.

The study presents complementary experiments and quantum chemical DFT computations to reveal the molecular-level interactions of an advanced nanomaterial, porphyrin aluminum metal-organic framework (compound 2), with the volatile organic sulfur compound diethyl sulfide (DES). First, the intermolecular host-guest interactions during the sorption of DES were explored under dynamic conditions, using the vapor of DES in flowing air. The in situ time-dependent ATR-FTIR spectroscopy in a controlled atmosphere was significantly improved though the use of a new facilely built spectroscopic mini-chamber. The binding site of DES in compound 2 involves the µ(O-H) and COO- groups of the linker of the sorbent. Further, the chemical kinetics of the sorption of DES was investigated, and it follows the Langmuir adsorption kinetic model. That is, depending on the time interval, the process obeys either the pseudo-first- or pseudo-second-order rate law. For the Langmuir adsorption of the pseudo-first order, the rate constant is robs = 0.165 ± 0.017 min-1. Next, the interaction of compound 2 with the saturated vapor of DES yields the adsorption complex compound 3 [Al-MOF-TCPPH2]2(DES)7. The adsorbed amount of DES is very large at 36.5 wt.% or 365 mg/g sorbent, one of the highest values reported on any sorbent. The molecular modes of bonding of DES in the complex were investigated through quantum chemical DFT computations. The adsorption complex was facilely regenerated by gentle heating. The advanced functional material in this work has significant potential in the environmental remediation of diethyl sulfide and related volatile organic sulfur compounds in air, and it is an interesting target of mechanistic studies of sorption.

Boron-based octahedral dication experimentally detected: DFT surface confirms its availability.

Borane and heteroborane clusters have been known as neutral or anionic species. In contrast to them, several ten-vertex monocationic nido and closo dicarbaborane-based systems have recently emerged from the reaction of the parent bicapped-square antiprismatic dicarbaboranes with N-heterocyclic carbenes followed by the protonization of the corresponding nido intermediates. The expansion of these efforts has afforded the very first closo-dicationic octahedral phosphahexaborane along with new closo-monocationic pnictogenahexaboranes of the same shapes. All are the products of the one-pot procedure that consists in the reaction of the same carbenes with the parent closo-1,2-Pn2B4Br4 (Pn = As, P). Whereas in the case of phosphorus such a monocation appears to be a mixture of stable intermediates, and arsenahexaboranyl monocation has occurred as the final product, all of them without using any subsequent reaction. The well-established DFT/ZORA/NMR approach has unambiguously confirmed the existence of these species in solution, and computed electrostatic potentials have revealed the delocalization of the positive charge in these monocations and in the very first dication, namely within the octahedral shapes in both cases.

Redox energetics of hypercloso boron hydrides B(n)H(n) (n = 6-13) and B12X12 (X = F, Cl, OH, and CH3).

The reduction potentials (E°(Red) versus SHE) of hypercloso boron hydrides B(n)H(n) (n = 6-13) and B(12)X(12) (X = F, Cl, OH, and CH(3)) in water have been computed using the Conductor-like Polarizable Continuum Model (CPCM) and the Solvation Model Density (SMD) method for solvation modeling. The B3LYP/aug-cc-pvtz and M06-2X/aug-cc-pvtz as well as G4 level of theory were applied to determine the free energies of the first and second electron attachment (ΔG(E.A.)) to boron clusters. The solvation free energies (ΔG(solv)) greatly depend on the choice of the cavity set (UAKS, Pauling, or SMD) while the dependence on the choice of exchange/correlation functional is modest. The SMD cavity set gives the largest ΔΔG(solv) for B(n)H(n)(0/-) and B(n)H(n)(-/2-) while the UAKS cavity set gives the smallest ΔΔG(solv) value. The E°(Red) of B(n)H(n)(-/2-) (n = 6-12) with the G4/M06-2X(Pauling) (energy/solvation(cavity)) combination agrees within 0.2 V of experimental values. The experimental oxidative stability (E(1/2)) of B(n)X(n)(2-) (X = F, Cl, OH, and CH(3)) is usually located between the values predicted using the B3LYP and M06-2X functionals. The disproportionation free energies (ΔG(dpro)) of 2B(n)H(n)(-) → B(n)H(n) + B(n)H(n)(2-) reveal that the stabilities of B(n)H(n)(-) (n = 6-13) to disproportionation decrease in the order B(8)H(8)(-) > B(9)H(9)(-) > B(11)H(11)(-) > B(10)H(10)(-). The spin densities in B(12)X(12)(-) (X = F, Cl, OH, and CH(3)) tend to delocalize on the boron atoms rather than on the exterior functional groups. The partitioning of ΔG(solv)(B(n)H(n)(2-)) over spheres allows a rationalization of the nonlinear correlation between ΔG(E.A.) and E°(Red) for B(6)H(6)(-/2-), B(11)H(11)(-/2-), and B(13)H(13)(-/2-).