Gas-phase Density Functional Theory Calculations Research Articles

Crystal structure and cation-anion interactions of potassium (Difluoromethanesulfonyl) (trifluorome thanesulfonyl)imide.

Sulfonimide salts are of great interest for battery use thanks to their special properties including sufficient superior chemical/thermal stabilities, structural flexibility, etc. In particular, the hydrogen-containing sulfonimide (difluoromethanesulfonyl)(trifluoromethanesulfonyl)imide anion {[N(SO2CF2H) (SO2CF3)]-, DFTFSI-}, stands out owing to its suppressed anion mobility and superior electrochemical properties. We herein report the structural analyses of potassium (difluoromethanesulfonyl)(trifluoromethanesulfonyl)imide {K [N(SO2CF2H) (SO2CF3)], KDFTFSI} by virtue of single crystal X-ray diffraction and computational approaches. Our results reveal that KDFTFSI crystallizes in a orthorhombic cell (space group: Pbcn) comprising of cationic and anionic layers, which is similar to the conventional sulfonimide salt, potassium bis(trifluoromethanesulfonyl)imide {K [N(SO2CF3)2], KTFSI}. Gas-phase density functional theory calculations show that the conversion from trans to cis DFTFSI- anions is hindered due to the presence of stabilizing intramolecular H-bonding interactions in the trans conformer; yet interaction with K+ substantially minimizes the energy difference between the two conformers due to the formation of strong tridentate K+ coordination with oxygen atoms in the cis KDFTFSI. This work is anticipated to provide further understanding on the structure-property relations of hydrogenated sulfonimide anions, and thus inspire the structural design of new anions for battery research.

Structures and Spin States of Iron(II) Complexes of Isomeric 2,6-Di(1,2,3-triazolyl)pyridine Ligands.

Iron(II) complex salts of 2,6-di(1,2,3-triazol-1-yl)pyridine (L1) are unexpectedly unstable in undried solvent. This is explained by the isolation of [Fe(L1)4(H2O)2][ClO4]2 and [Fe(NCS)2(L1)2(H2O)2]·L1, containing L1 bound as a monodentate ligand rather than in the expected tridentate fashion. These complexes associate into 44 grid structures through O-H···N hydrogen bonding; a solvate of a related 44 coordination framework, catena-[Cu(μ-L1)2(H2O)2][BF4]2, is also presented. The isomeric ligands 2,6-di(1,2,3-triazol-2-yl)pyridine (L2) and 2,6-di(1H-1,2,3-triazol-4-yl)pyridine (L3) bind to iron(II) in a more typical tridentate fashion. Solvates of [Fe(L3)2][ClO4]2 are low-spin and diamagnetic in the solid state and in solution, while [Fe(L2)2][ClO4]2 and [Co(L3)2][BF4]2 are fully high-spin. Treatment of L3 with methyl iodide affords 2,6-di(2-methyl-1,2,3-triazol-4-yl)pyridine (L4) and 2-(1-methyl-1,2,3-triazol-4-yl)-6-(2-methyl-1,2,3-triazol-4-yl)pyridine (L5). While salts of [Fe(L5)2]2+ are low-spin in the solid state, [Fe(L4)2][ClO4]2·H2O is high-spin, and [Fe(L4)2][ClO4]2·3MeNO2 exhibits a hysteretic spin transition to 50% completeness at T1/2 = 128 K (ΔT1/2 = 6 K). This transition proceeds via a symmetry-breaking phase transition to an unusual low-temperature phase containing three unique cation sites with high-spin, low-spin, and 1:1 mixed-spin populations. The unusual distribution of the spin states in the low-temperature phase reflects "spin-state frustration" of the mixed-spin cation site by an equal number of high-spin and low-spin nearest neighbors. Gas-phase density functional theory calculations reproduce the spin-state preferences of these and some related complexes. These highlight the interplay between the σ-basicity and π-acidity of the heterocyclic donors in this ligand type, which have opposing influences on the molecular ligand field. The Brønsted basicities of L1-L3 are very sensitive to the linkage isomerism of their triazolyl donors, which explains why their iron complex spin states show more variation than the better-known iron(II)/2,6-dipyrazolylpyridine system.

Twisted and Bent Out of Shape: Symmetry and Chirality Analysis of Substituted Ferrocenes

Ferrocene symmetry is commonly described as either eclipsed (D5h) or staggered (D5d), but this symmetry does not hold when substitution is involved. Here we examine and quantify the effect of substitution on the geometry of the core structure of ferrocene, and provide means to distinguish between its various distortion paths. Continuous symmetry analysis of the core structure of 7418 substituted ferrocenes extracted from the Cambridge Crystallographic Database was used to explore its twisting and bending distortion paths, as well as asymmetric bond stretch that deforms the symmetry of its cyclopentadienyl rings. Gas-phase density functional theory calculations provided a theoretical background to describe these distortion paths and define symmetry profiles for conformer interconversion processes and the interplay between them. Our results show that the distortion of ferrocene can often be substantial. Furthermore, its geometry is highly flexible, and almost always chiral to some degree. Handedness in term...

Iron(II) Complexes of 2,4-Dipyrazolyl-1,3,5-triazine Derivatives—The Influence of Ligand Geometry on Metal Ion Spin State

Seven [FeL2][BF4]2 complex salts were prepared, where L is a 6-substituted 2,4-di(pyrazol-1-yl)-1,3,5-triazine (bpt) derivative. The complexes are all crystallographically high-spin, and exhibit significant distortions from an ideal D2d-symmetric coordination geometry. In one case, an unusual type of metal ion disorder was observed among a cubic array of ligands in the crystal lattice. The complexes are also high-spin between 3 and 300 K in the solid state and, where measured, between 239 and 333 K in CD3CN solution. This result is unexpected, since homoleptic iron(II) complexes of related 2,6-di(pyrazol-1-yl)pyridine, 2,6-di(pyrazol-1-yl)pyrazine, and 2,6-di(pyrazol-1-yl)pyrimidine derivatives often exhibit thermal spin-crossover behavior. Gas-phase density functional theory calculations confirm the high-spin form of [Fe(bpt)2]2+ and its derivatives is stabilized relative to iron(II) complexes of the other ligand types. This reflects a weaker Fe/pyrazolyl σ-bonding interaction, which we attribute to a small narrowing of the chelate ligand bite angle associated with the geometry of the 1,3,5-triazinyl ring. Hence, the high-spin state of [Fe(bpt)2]2+ centers does not reflect the electronic properties of its heterocyclic ligand donors but is imposed by the bpt ligand conformation. A high-spin homoleptic iron(III) complex of one of the bpt derivatives was also synthesized.

Quantum Mechanical Investigation of Proton Transport in Imidazolium Methanesulfonate Ionic liquid

Protic ionic liquids (PIL) are promising anhydrous proton conductors for fuel cell applications especially at higher temperature. In this study, quantum chemistry calculations using density functional theory (DFT) were performed to investigate proton conduction in imidazolium methanesulfonate (IMMSA) PIL on interaction with varying imidazole (IM) concentration. These investigations include the extent of proton transfer (PT) from methanesulfonic acid to the imidazole base and calculation of various energy barriers of PT. The results show that the difference in gas phase proton affinity (ΔPA) of the anion and base is a reliable predictor of the extent of proton transfer from acid to base, and ΔPA values <90 kcal/mol indicates facile PT. These gas phase DFT calculations show that, on addition of at least one IM to IMMSA, proton dissociates from MSA to IM leading to the generation of charged species, cations and anions, essential for proton conduction. The PT barrier from IMH+ to IM reduces with IM molecules ...

Real-space visualization of conformation-independent oligothiophene electronic structure.

We present scanning tunneling microscopy and spectroscopy (STM/STS) investigations of the electronic structures of different alkyl-substituted oligothiophenes on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes adopted distinct straight and bent conformations. By combining STS maps with STM images, we visualize, in real space, particle-in-a-box-like oligothiophene molecular orbitals. We demonstrate that different planar conformers with significant geometrical distortions of oligothiophene backbones surprisingly exhibit very similar electronic structures, indicating a low degree of conformation-induced electronic disorder. The agreement of these results with gas-phase density functional theory calculations implies that the oligothiophene interaction with the Au(111) surface is generally insensitive to molecular conformation.

Unraveling Interactions in Molecular Crystals Using Dispersion Corrected Density Functional Theory: The Case of the Epoxydihydroarsanthrene Molecules.

Noncovalent interactions are prevalent in crystal packing and supramolecular chemistry. Directional noncovalent interactions such as donor-acceptor bonds (e.g., hydrogen, chalcogen, and pnictogen bonds) as well as nondirectional forces (such as dispersion) come together to stabilize supramolecular assemblies by striking a delicate energetic balance. Typically, a two-pronged approach employing experimental X-ray structures and gas phase quantum chemical modeling has been used to understand and design supramolecular architectures. Drawing from recent advances in molecular crystal modeling with dispersion corrected density functional theory (DFT), we propose in this article a combination of qualitative noncovalent index (NCI) analysis and periodic and gas phase DFT calculations on substitutional crystal analogues to unravel the dominant interactions in a particular crystal packing. We illustrate the possibilities of this approach by studying three crystal packings of epoxydihydroarsanthrene analogues that present a complex combination of donor-acceptor interactions including pnictogen-pnictogen, pnictogen-π, and pnictogen-chalcogen. We show that, in these crystals, the chalcogen-pnictogen interaction dominates over the pnictogen-pnictogen and pnictogen-π. In the latter, the role of donor and acceptor is reversed depending on the interacting moieties. Multiple chalcogen-pnictogen interactions necessitate larger donor atoms, such as sulfur. These observations explain and rationalize the experimentally observed crystal structures.

Molecular interactions of alcohols with zeolite BEA and MOR frameworks

Zeolites can adsorb small organic molecules such as alcohols from a fermentation broth. Also in the zeolite-catalyzed conversion of alcohols to biofuels, biochemicals, or gasoline, adsorption is the first step. Several studies have investigated the adsorption of alcohols in different zeolites experimentally, but computational investigations in this field have mostly been restricted to zeolite MFI. In this study, the adsorption of C1-C4 alcohols in BEA and MOR was investigated using density functional theory (DFT). Calculated adsorption geometries and the corresponding energies of the designed cluster models were comparable to periodic calculations, and the adsorption energies were in the same range as the corresponding computational and experimental values reported in the literature for zeolite MFI. Thus, BEA and MOR may be good adsorption materials for alcohols in the field of downstream processing and catalysis. Aside from the DFT calculations, adsorption isotherms were determined experimentally in this study from aqueous solutions. For BEA, the adsorption of significant amounts of alcohol from aqueous solution was observed experimentally. In contrast, MOR was loaded with only a very small amount of alcohol. Although differences were found between the affinities obtained from gas-phase DFT calculations and those observed experimentally in aqueous solution, the computational data presented here represent molecular level information on the geometries and energies of C1-C4 alcohols adsorbed in zeolites BEA and MOR. This knowledge should prove very useful in the design of zeolite materials intended for use in adsorption and catalytic processes, as it allows adsorption behavior to be predicted via judiciously designed computational models.

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions.

Density functional theory (DFT) based quantum mechanical/molecular mechanical (QM/MM) calculations have provided valuable insight into the reactivity of the cytochrome P450 family of enzymes (P450s). A failure of commonly used DFT methods, such as B3LYP, is the neglect of dispersion interactions. An empirical dispersion correction has been shown to improve the accuracy of gas phase DFT calculations of P450s. The current work examines the effect of the dispersion correction in QM/MM calculations on P450s. The hydrogen abstraction from camphor, and hydrogen abstraction and C-O addition of cyclohexene and propene by P450cam have been modeled, along with the addition of benzene to Compound I in CYP2C9, at the B3LYP-D2/CHARMM27 level of theory. Single point energy calculations were also performed at the B3LYP-D3//B3LYP-D2/CHARMM27 level. The dispersion corrections lower activation energy barriers significantly (by ∼5 kcal/mol), as seen for gas phase calculations, but has a small effect on optimized geometries.These effects are likely to be important in modeling reactions catalyzed by other enzymes also. Given the low computational cost of including such dispersion corrections, we recommend doing so in all B3LYP based QM/MM calculations.

Configurations and conformations of glycosyl sulfoxides

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

Theoretical studies on the pKa values of perfluoroalkyl carboxylic acids

Abstract Computational studies were conducted using the major levels of semiempirical, ab initio, density functional theory (DFT), and the CBS-Q//B3 method and various solvation models on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C 1 (trifluoroacetic acid) to C 9 ( n -perfluorodecanoic acid) as well as the monomethyl branched C 7 ( n -perfluorooctanoic acid; n -PFOA) isomers. Regardless of perfluoroalkyl chain length and theoretical method employed, application of a computational thermodynamic cycle indicated no significant change in the estimated aqueous monomeric p K a values between C 1 and C 9 , all having a relatively constant p K a of about 0 that is in agreement with earlier predictions and recent experimental evidence. Perfluoroalkyl chain helicity does not appear to result in increased monomeric PFCA p K a values at chain lengths greater than 5. Increasing chain length does not substantially influence the structural or electronic character of the carboxylic acid head group. A MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n -PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to DFT investigations. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the conformers, gave conformationally averaged p K a values for n -PFOA equal to the global minimum helical conformer p K a . The conformational populations under study occupy ∼100% of the global n -PFOA conformational space, indicating no higher energy/low acidity conformations remain unexamined that could influence the predicted composite aqueous monomeric p K a of zero for this compound.

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids

AbstractComputational studies were conducted using the major levels of semiempirical, ab initio, density functional theory (DFT), and the CBS-Q//B3 method and various solvation models on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C~1~ (trifluoroacetic acid) to C~9~ (n-perfluorodecanoic acid) as well as the monomethyl branched C~7~ (n-perfluorooctanoic acid; n-PFOA) isomers. Regardless of perfluoroalkyl chain length and theoretical method employed, application of a computational thermodynamic cycle indicated no significant change in the estimated aqueous monomeric pK~a~ values between C~1~ and C~9~, all having a relatively constant pK~a~ of about 0 that is in agreement with earlier predictions and recent experimental evidence. Perfluoroalkyl chain helicity does not appear to result in increased monomeric PFCA pK~a~ values at chain lengths greater than 5. Increasing chain length does not substantially influence the structural or electronic character of the carboxylic acid head group. A MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to DFT investigations. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the conformers, gave conformationally averaged pK~a~ values for n-PFOA equal to the global minimum helical conformer pK~a~. The conformational populations under study occupy about 100 percent of the global n-PFOA conformational space, indicating no higher energy/low acidity conformations remain unexamined that could influence the predicted composite aqueous monomeric pK~a~ of zero for this compound.

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA)

AbstractA molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pK~a~ values) for a final converged set of twelve n-PFOA conformers, including the global minimum helical perfluoroalkyl chain geometry and eleven non-helical higher energy conformations. Collectively, the twelve lowest energy conformers appear to completely encompass the global conformational space for n-PFOA, indicating no higher energy conformations likely remain that could appreciably influence the observed composite aqueous pK~a~ of this compound. The estimated pK~a~ values of all eleven non-helical n-PFOA conformers were within 0.1 pK~a~ units of the helical conformer pK~a~. The findings support previous predictions and recent experimental evidence for an aqueous phase n-PFOA monomeric pK~a~ of about zero.

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA)

AbstractA molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pK~a~ values) for a final converged set of twelve n-PFOA conformers, including the global minimum helical perfluoroalkyl chain geometry and eleven non-helical higher energy conformations. Collectively, the twelve lowest energy conformers appear to encompass 85% of the total conformational space for n-PFOA, indicating no higher energy conformations likely remain that could appreciably influence the observed composite aqueous pK~a~ of this compound. The estimated pK~a~ values of all eleven non-helical n-PFOA conformers were within 0.2 pK~a~ units of the helical conformer pK~a~. The findings support previous predictions and recent experimental evidence for an aqueous phase n-PFOA monomeric pK~a~ of about zero.

Phosphines Bearing Alkyne Substituents: Synthesis and Hydrophosphination Polymerization

A synthetic route is described for a series of phosphines bearing pendant alkyne substituents, from the conversion of BrC(6)H(2)R(2)C[triple bond]CR' (R = Me, i-Pr; R' = Ph, SiMe(3)) to [(mu-Br)Cu(Et(2)N)(2)PC(6)H(2)R(2)C[triple bond]CR'](2) and subsequently to Cl(2)PC(6)H(2)R(2)C[triple bond]CR' and H(2)PC(6)H(2)R(2)C[triple bond]CR'. Lithiation and subsequent alkylation yield the secondary phosphines R(H)PC(6)H(2)(i-Pr)(2)C[triple bond]CPh (R = CH(2)i-Pr, CH(2)Ph). Intermolecular hydrophosphination-polymerization is used to prepare the polymeric species [RPC(6)H(2)(i-Pr)(2)CH=CPh](n), which can then be sulfurized to give [RP(S)C(6)H(2)(i-Pr)(2)CH=CPh](n). The polymeric products were characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and gel permeation chromatography. These data indicate a degree of polymerization (DP(n)) of up to 60. Discussion of the mechanism is augmented with gas-phase density functional theory calculations.

Correlation between computed gas‐phase and experimentally determined solution‐phase infrared spectra: Models of the iron–iron hydrogenase enzyme active site

Gas-phase density functional theory calculations (B3LYP, double zeta plus polarization basis sets) are used to predict the solution-phase infrared spectra for a series of CO- and CN-containing iron complexes. It is shown that simple linear scaling of the computed C--O and C--N stretching frequencies yields accurate predictions of the the experimentally determined nu(CO) and nu(CN) values for a variety of complexes of different charges and in solvents of varying polarity. As examples of the technique, the resulting correlation is used to assign structures to spectroscopically observed but structurally ambiguous species in two different systems. For the (mu-SCH2CH2CH2S)[Fe(CO)3]2 complex in tetrahydrofuran solution, our calculations show that the initial electrochemical reduction process leads to a simple one-electron reduced product with a structure very similar to the (mu-SCH2CH2CH2S)[Fe(CO)3]2 parent complex. For the iron-iron hydrogenase enzyme active site, our computations show that the absence or presence of a water molecule near the distal iron center (the iron center further from the [4Fe4S] cluster and protein backbone) has very little effect on the predicted infrared spectra.

An experimental and computational evaluation of the energetics of the isomeric methoxyphenylcarbenes generated in carbon atom reactions.

Carbon atom reactions with anisole and methoxybenzaldehyde demonstrate the reversible ring expansion of methoxyphenylcarbene (CH(3)O-C(6)H(4)-C-H). Trapping with HBF(4) yields the methoxytropylium ion, analogous to the well-known reactions of phenylcarbene. For instance, in the reaction of carbon atom with p-methoxybenzaldehyde, which proceeds by deoxygenation of the carbonyl group and formation of the corresponding arylcarbene, the products formed are methoxytropylium fluoroborate, p-methoxytoluene and m-methoxytoluene in yields of 69.4, 7.6, and 22.9%, respectively. Gas-phase density functional theory calculations were also carried out. The observed product yields from the uniquely generated p- and m-methoxyphenylcarbenes are in good agreement with the calculations. In the case of o-methoxyphenylcarbene, however, the calculations indicate that formation of dihydrobenzofuran is the most facile rearrangement on the ground-state singlet surface. In contrast, ring expansion is observed to be the major reaction path experimentally. The exothermicity of the deoxygenation step for carbon atom reaction with methoxybenzaldehyde ( approximately 100 kcal/mol) can allow for an excited singlet state to be formed initially. This excited singlet state of the methoxyphenylcarbene will resemble open-shell phenylnitrene, which is known to undergo ring expansion much more readily than phenylcarbene. On the basis of this analogy, we reconcile the difference in reactivity of the arylcarbene predicted by density functional theory calculations with the reactivity observed experimentally.