Amine-tetrachloromethane charge transfer complexes: a structural and computational study

Abstract

Amine-tetrachloromethane charge-transfer complexes have recently been shown to be useful intermediates in transition-metal free solar light-assisted organic synthetic chemistry. Of particular promise is the complex of 1,4-diazabicyclo[2.2.2]octane (DABCO) which may serve as a starting point for several potential reactions involving oxidation of organic compounds. Here we disclose the crystal structure of the [DABCO???CCl₄] complex, and computational studies of two possible complex structures in their ground state, as well as in their first singlet and first triplet excited states.     

The SAMP alkylation: a computational study

In a computational study of a stereoselective C-C bond formation, the SAMP alkylation, a previously proposed S(E)2'-front mechanism is evaluated taking into account all current experimental evidence. Using semiempirical, density functional and perturbation theoretical methods, the structure of the key intermediate is revealed and the metalloretentive nature of the mechanism is explained. The experimental ee values of a range of reactions with different electrophiles and carbonyl sources can be correlated with calculated differences in activation energies. Furthermore, it can be concluded that the selectivity derives from the internal stabilization of the transition state 3_syn (corresponding to an electrophilic attack from above the lithiohydrazone plane) by electrophile-lithium interactions. The fast computational approach can be used best as a screening method which excludes less promising candidates to guide this synthetic method.     

Isostructural potassium and thallium salts of sterically crowded triazenes: a structural and computational study

Because of their similar cationic radii, potassium and thallium(I) compounds are usually regarded as closely related. Homologous molecular species containing either K(+) or Tl(+) are very rare, however. We have synthesized potassium and thallium salts MN3RR' derived from the biphenyl- or terphenyl-substituted triazenes Tph2N3H (1a), Dmp(Mph)N3H (1b), Dmp(Tph)N3H (1c), and (Me4Ter)2N3H (1d) (Dmp=2,6-Mes 2C6H3 with Mes=2,4,6-Me3C6H2; Me4Ter=2,6-(3,5-Me2C6H3)2C6H3; Mph=2-MesC6H4; Tph=2-TripC6H4 with Trip=2,4,6-(i)Pr3C6H2). The potassium complexes 2a- d were obtained in almost quantitative yield from the reaction of 1a- d with potassium metal in n-heptane. Metalation of 1a- d with TlOEt afforded the thallium triazenides 3a- d in high yields. All new compounds have been characterized by (1)H and (13)C NMR spectroscopy, elemental analysis, and X-ray crystallography and for selected species by melting point (not 3b), IR spectroscopy (2a, 2d, 3a, 3c, 3d), and mass spectrometry (2a, 3c). In the solid-state structures of monomeric 2a and 3a, quasi-monomeric 2b, 3b, 2c, and 3c, and dimeric 2d and 3d additional metal-eta (n)-pi-arene-interactions to the flanking arms of the biphenyl- and terphenyl groups in the triazenide ligands of decreasing hapticity n are observed. Remarkably, all homologous potassium and thallium complexes crystallize in isomorphous cells. For 2a and 3a, the nature of the M-N and M...C(arene) bonding was studied by density functional theory calculations.     

The generation of diazirinone: a computational study

Computational studies indicate that the reaction of p-nitrophenoxyfluorodiazirine with fluoride ion should generate diazirinone. However, fluoride ion also catalyzes the decomposition of diazirinone to carbon monoxide and nitrogen, so that the diazirinone is likely to be unstable to the conditions used to generate it.     

Solvation and structural effects on the stability of 10-X-2 ate-complexes: a computational study

The structures and energies of a variety of 10-X-2 ate-complexes derived from reaction of alkyllithiums and aryllithiums with the corresponding organohalides have been studied at the B3LYP/6-31+2G** theoretical level. The results of the calculations, which are in good agreement with the available experimental data, indicate that diaryl ate-complexes are more stable than their dialkyl counterparts. Fluorine substitution was found to confer substantial stability to both diaryl and dialkyl ate-complexes, and the calculations suggest that perfluoro dialkyl 10-X-2 ate-complexes should be experimentally observable species. One of the most important factors contributing to stability of a 10-X-2 ate-complex is removal of the formally cationic lithium from the vicinity of the ate-anion via coordination with a Lewis basic solvent.     

A structural and computational study of citrulline in biochemical reactions

Structural Chemistry - Citrulline, a non-essential amino acid, is used therapeutically in mitochondrial diseases, especially since it is a well-tolerated medicinal compound. Athletes use citrulline...     

An ab initio structural and vibrational analysis of gauche,trans,trans- and gauche,cis,trans-hexa-1,3,5-trienes

The results of complete geometry optimizations of the high energy stable gauche,Trans,trans- and gauche,Cis,trans- rotamers of hexa-1,3,5-trienes are reported at the RHF/6-31G//RHF/B-31G level. The angles of rotation around one of the single C-C bonds are found to be 33.7° and 45.5°, respectively. The corresponding harmonic force fields of these molecules are also reported at this level and corrected using scale factors transferred from buta 1,3-diene. Aspecial scale factor was used for the central C=C double bond stretching coordinate to take into account vibronic coupling. The theoretical vibrational frequencies, calculated with the scaled quantum mechanical (SQM) force fields, allow a complete interpretation of the experimental vibrational spectra of these molecules.Preliminary results were reported at the Austin XII Symposium on Molecular Structure, Austin, TX, February 28 through March 3, 1988, S 18, p. 111 (USA) and at the XIXth European Congress on Molecular Spectroscopy, Dresden, September 4 through September 8, 1989, p. 226 (GDR).     

Monosilicon-substituted cyanoacetylene: a computational study

A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.     

The carboxylate shift in zinc enzymes: a computational study

Zinc is the second most abundant transition element in biology and the only metal known to be represented in enzymes from each one of the six classes established by the International Union of Biochemistry. The flexible coordination geometry, the fast ligand exchange, the lack of redox activity, and its role as Lewis acid are just some of the features that make zinc an invaluable element in biological catalysis. In this study, we have analyzed the importance in mononuclear Zn enzymes of an interesting mechanistic phenomenon known as carboxylate shift, which is characterized by a change in the coordination mode of a carboxylate group (mono to bidentate or vice versa) with both ligand entrance or exit from the metal coordination sphere. Using B3LYP calculations, we were able to unveil in detail patterns relating the intrinsic characteristics of a given Zn coordination sphere with the existence or not of a carboxylate-shift mechanism and the additional energy stabilization arising from it. In particular, a specific Zn coordination sphere containing a carboxylate ligand (Asp or Glu), a cysteine, and a histidine has been shown to have the most favorable combination of amino acid residues that ensures a fast ligand exchange.     

Maya blue: a computational and spectroscopic study

Maya Blue pigment, used in pre-Colombian America by the ancient Mayas, is a complex between the clay palygorskite and the indigo dye. The pigment can be manufactured by mixing palygorskite and indigo and heating to T > 120 degrees C. The most quoted hypothesis states that the dye molecules enter the microchannels which permeate the clay structure, thus creating a stable complex. Maya Blue shows a remarkable chemical stability, presumably caused by interactions formed between indigo and clay surfaces. This work aims at studying the nature of these interactions by means of computational and spectroscopic techniques. The encapsulation of indigo inside the clay framework was tested by means of molecular modeling techniques. The calculation of the reaction energies confirmed that the formation of the clay-organic complex can occur only if palygorskite is heated at temperatures well above the water desorption step, when the release of water is entropically favored. H-bonds between the clay framework and the indigo were detected by means of spectroscopic methods. FTIR spectroscopy on outgassed palygorskite and freshly synthesized Maya Blue samples showed that the presence of indigo modifies the spectroscopic features of both structural and zeolitic water, although no clear bands of the dye groups could be observed, presumably due to its very low concentration. The positions and intensities of delta(H2O) and nu(H2O) modes showed that part of the structural water molecules interact via a hydrogen bond with the C=O or N-H groups of indigo. Micro-Raman spectra clearly evidenced the presence of indigo both in original and in freshly synthesized Maya Blue. The nu(C=O) symmetric mode of Maya Blue red-shifts with respect to pure indigo, as the result of the formation of H-bonds with the nearest clay structural water. Ab initio quantum methods were applied on the indigo molecule, both isolated and linked through H-bonds with water, to calculate the magnitude of the expected vibrational shifts. Calculated and experimental vibrational shifts appeared to be in good agreement. The presence of a peak at 17.8 ppm and the shift of the N-H signal in the 1H MAS NMR spectrum of Maya Blue provide evidence of hydrogen bond interactions between indigo and palygorskite in agreement with IR and ab initio methods.     

The "azido gauche effect"-implications for the conformation of azidoprolines

The "azido gauche effect" was examined both experimentally and theoretically and was found to determine the conformation of, for example, (4R)- and (4S)-azidoproline (Azp) derivatives. For (4R)Azp derivatives, the azido gauche effect induces a preferred C(4)-exo conformation of the pyrrolidine ring, which leads to stabilization of the s-trans amide conformer of, e.g., Ac-(4R)Azp-OCH(3) (5R) via an n-->pi interaction between the nonbonding electrons of the oxygen of the acetyl group and the carbonyl group of the ester. For (4S)Azp derivatives, the azido gauche effect results in a C(4)-endo conformation of the pyrrolidine ring that does not allow for this stabilizing n-->pi interaction of the s-trans conformer. Consequently, a significantly higher s-trans:s-cis amide conformer ratio is observed for (4R)Azp compared to (4S)Azp derivatives (e.g., 6.1:1 versus 2.6:1 in D(2)O for Ac-(4R)Azp-OCH(3) (5R) compared to Ac-(4S)Azp-OCH(3) (5S)). These conformational preferences are reflected in the higher tendency of (4S)Azp-containing peptides to form cyclic peptides with all-cis amide bonds compared to (4R)Azp derivatives. Ab initio calculations demonstrate that the strength of the azido gauche effect is comparable to that of the well-known "fluorine gauche effect". For azidoethane derivatives N(3)-CH(2)CH(2)-X (X = N(3), NHCOH, NHAc, or N(CH(3))Ac), the ab initio calculations revealed energy differences of 5-13 kJ mol(-)(1) between the anti and gauche conformations in favor of the gauche conformer. Calculations were also performed for the (4R)Azp and (4S)Azp derivatives 5R and 5S, supporting the experimentally observed data.     

The energetic and structural effects of steric crowding in phosphate and dithiophosphinate complexes of lanthanide cations M3+: a computational study

Metal-ligand binding strength and selectivity result from antagonistic metal-ligand M-L attractions and ligand-ligand L-L repulsions. On the basis of quantum-mechanical (QM) calculations on lanthanide complexes, we show that this interplay determines the binding affinities in the gas phase. In the series of [ML3] complexes (M = La, Eu, and Yb) with negatively charged phosphoryl ligands L- = (MeO)2PO2- and Me2PS2-, the binding energies follow the order Yb3+ > Eu3+ > La3- for a given ligand, and (MeO)2PO2- > Me2PS2- for a given cation. However, adding a neutral LH ligand to [ML3] changes the order to Eu3+ > Yb3+ > La3+ for the oxygen ligand and La3+ > Eu3- > Yb3+ for the sulfur ligand, indicating that steric strain in the first coordination sphere is largest for the smallest cation and for sulfur binding sites. We investigated the question of additional hydration of the [ML3LH] complexes in aqueous solution by molecular dynamics (MD) simulations, using two sets of atomic charges. It was found that pairwise additive potentials overestimate the coordination and hydration numbers of the cations, while adding polarization energy terms for the ligands yields better agreement between QM and MD results and supports the concept of steric strain in the first coordination sphere.     

The reaction of triplet nitrenes with oxygen: a computational study

Triplet carbenes react much more rapidly with oxygen than do triplet nitrenes. This trend is explained by DFT and MO calculations. [reaction: see text]     

Formamide dimers: a computational and matrix isolation study

The dimerization of formamide (FMA) has been investigated by matrix isolation spectroscopy, static ab initio calculations, and ab initio molecular dynamics (AIMD) simulations. Comparison of the experimental matrix IR spectra with the ab initio calculations reveals that two types of dimers A and C are predominantly formed, with two and one strong NH...O hydrogen bonds, respectively. This is in accordance with previously published experiments. In addition, there is also experimental evidence for the formation of the thermally labile dimer B after deposition of high concentrations of FMA in solid xenon. The AIMD simulations of the aggregation process show that in all cases dimer C is initially formed, but rearrangement to the more stable doubly hydrogen-bonded structures A or B occurs for a fraction of collisions on the sub-picosecond time scale.     

Integrated NMR and computational study of push-pull NLO probes: interplay of solvent and structural effects

In this study we combined QM calculations and NMR measurements to understand at a detailed level the complex interplay of structural/electronic properties with the effects of the solvent in the NLO activity of push-pull systems, quantified in terms of variations of the static hyperpolarizability. Different parameters (bond lengths and bond length alternation, vibrational frequencies, electronic charge distribution) are introduced and tested to rationalize both the solvent sensitivity of three molecular systems (namely, p-nitroaniline, ethyl 4-ammino benzoate, and 5-nitro-1H-indole) and the differences among them. This analysis has finally allowed us to establish a clear correlation between the charge transfer behavior of the systems, their NLO properties, and NMR parameters also validating simplified but effective chemical analyses based on resonance limit forms.     

The effect of reduction on rhenium(I) complexes with binaphthyridine and biquinoline ligands: a spectroscopic and computational study

A number of rhenium complexes with binaphthyridine and biquinoline ligands have been synthesized and studied. These are [Re(L)(CO)3Cl] where L = 3,3'-dimethylene-2,2'-bi-1,8-naphthyridine (dbn), 2,2'-bi-1,8-naphthyridine (bn), 3,3'-dimethylene-2,2'-biquinoline (dbq), and 3,3'-dimethyl-2,2'-biquinoline (diq). This series represents ligands in which the electronic properties and steric preferences are tuned. These complexes are modeled using density functional theory (DFT). An analysis of the resonance Raman spectra for these complexes, in concert with the vibrational assignments, reveals that the accepting molecular orbital (MO) in the metal-to-ligand charge transfer (MLCT) transition is the LUMO and causes bonding changes at the inter-ring section of the ligand. The electronic absorption spectroelectrochemistry for the reduced complexes of [Re(dbn)(CO)3Cl], [Re(dbq)(CO)3Cl], and [Re(diq)(CO)3Cl] suggest that the singly occupied MO is delocalized over the entire ligand structure despite the nonplanar nature of the diq ligand in [Re(diq)(CO)3Cl]. The IR spectroelectrochemistry for [Re(dbn)(CO)3Cl], [Re(dbq)(CO)3Cl], and [Re(bn)(CO)3Cl] reveal that reduction lowers the CO ligand vibrational frequencies to a similar extent in all three complexes. The substitution of naphthyridine for quinoline has little effect on the nature of the singly occupied MO. These data are supported by DFT calculations on the reduced complexes, which reveal that the ligands are flattened out by reduction: This may explain the similarity in the properties of the reduced complexes.     

Non-catalytic hydroamination of alkenes: a computational study

The detailed reaction profiles of the neutral-neutral as well as the cation-neutral direct hydroamination reactions between ethylene and ammonia are analyzed using MP2 (Full)/6-31++G(2df,2p) and B3LYP/6-31++G(2df,2p) methodologies. Analysis shows that both neutral-neutral, as well as the cation-neutral reactions are exothermic and the latter is >100 kJ/mol more exothermic than the former. Calculations show that a very large barrier height (>200 kJ/mol), and very large negative reaction entropy prevent the neutral-neutral reaction from proceeding in the forward direction. Analysis of the cation-neutral reaction, which is barrierless (the transition state is more stable than the reactants) and highly exothermic, indicates that the direct hydroamination reaction is thermodynamically attainable via a cation-neutral reaction pathway without a catalyst. Our calculations also suggest that although the cation-neutral direct hydroamination reaction is very fast, the cation of either ethylene or ammonia goes through a structural relaxation process before reacting with the other neutral reactant.     

Thermolysis of 2-methyloxetane: a computational study

Thermal fragmentation of 2-methyloxetane (2MO), which yields two different sets of products by virtue of ring asymmetry, was studied theoretically by using DFT, MPn and CASPT2//CASSCF methods. At the MPn and DFT theoretical levels, only concerted transition states were located on the ground state potential energy surface (PES). The CASSCF approach leads to different stepwise pathways for the two fragmentation modes, with biradical as intermediates, in addition to the concerted paths, with a very shallow PES for the asynchronous region in which intermediates becomes unstable under CASPT2//CASSCF calculations. Nevertheless, activation barriers thus calculated were quite consistent with experimental values. The reaction pathway that experimentally renders the main set of products was calculated as the lowest-energy path for the fragmentation of the 2-methyloxetane heterocycle, and this evolves with an initial cleavage of the C–O bond of the oxetane ring.     

Dichlorocarbene addition to cyclopropenes: a computational study

Reaction paths for addition of dichlorocarbene to 1,2-disubstituted cyclopropenes were calculated using hybrid density functional theory (B3LYP/6-31G) in the gas phase and in the presence of a continuum solvation model corresponding to acetonitrile. In both the gas phase and acetonitrile, :CCl2-cyclopropene addition follows an asymmetric, non-least-motion approach. Barriers to addition range from 0 to 2 kcal/mol. The reactions proceed in concerted fashion in both the gas phase and solution to yield 1,3-dienes or bicyclobutanes. The reaction pathway on this complex potential energy surface of this reaction appears to bifurcate, and the product distribution is believed to be controlled by reaction dynamics. At the present level of theory, there appears to be no minimum on the potential energy surface corresponding to a dipolar intermediate.