An ab initio and density functional theory study of the structure and bonding of sulfur ylides

Sulfur ylides are useful synthetic intermediates that are formed from the interaction between singlet carbenes and sulfur-containing molecules. Partial double-bond character frequently has been proposed as a key contributor to the stability of sulfur ylides. Calculations at the B3LYP, MP2, and CCSD(T) levels of theory employing various basis sets have been performed on the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) in order to investigate the structure and bonding of these systems. The following general properties of sulfur ylides were observed from the computational studies: C-S bond distances that are close in length to that of a typical C-S double bond, high charge transfer from the sulfide to the carbene, and large torsional rotation barriers. Analysis of the sulfur ylide charge distribution indicates that the unusually short C-S bond distance can be attributed in part to the electrostatic attraction between highly oppositely charged carbon and sulfur atoms. Furthermore, n --> sigma* stabilization arising from donation of electron density from the carbon lone pair orbital into S-H or S-C antibonding orbitals leads to larger than expected torsional barriers. Finally, natural resonance theory analysis indicates that the bond order of the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) is 1.4-1.5, intermediate between a single and double bond.     

Conjugation and hyperconjugation in conformational analysis of cyclohexene derivatives containing an exocyclic double bond

The equilibrium geometry, ring-inversion pathway barriers for analogues of cyclohexene with an exocyclic double bond have been studied using the MP2/6-311 G(d,p) level of theory. The equilibrium conformation of the ring depends on conjugation between the endocyclic and exocyclic double bonds. Interactions between conjugated double bonds include the pi-pi conjugation and interactions between the lone pair of the heteroatom of the exocyclic double bond and the sigma-antibonding orbital of the endocyclic single bond. In the case of the tetrahydrocycles with double bonds separated by a methylene group the balance between the pi --> sigma* hyperconjugation interactions between the exocyclic double bond and the neighboring methylene group and the n --> sigma* interaction between the lone pair of the heteroatom and the sigma-antibonding orbitals of the C(sp(2))-C(sp(3)) bond determine the geometrical parameters of the ring. The character of the potential-energy surface around the saddle point depends on the position of the exocyclic double bond and the orientation of the hydrogen atom attached to the heteroatom of the V group of the periodic table in the tetrahydrocycles with double bonds separated by a methylene group.     

Experimental and theoretical studies on the organic-inorganic hybrid compound: aluminum-NTCDA Co-deposited film

Electronic absorption, Fourier transform-infrared (FT-IR), and electron spin resonance spectra of aluminum-naphthalene tetracarboxylic dianhydlide (Al-NTCDA) co-deposited film have been measured at room temperature, and hybrid density functional theory (DFT) calculations have been carried out in order to elucidate the electronic states for the ground and low-lying excited states of the complexes. After the interaction of NTCDA with Al atom, the new electronic transition bands were appeared at near-IR region. The C=O stretching modes of NTCDA are red-shifted by the interaction with Al. From the DFT calculations, it was found that the electronic state of the complex at the ground state is characterized by a slight charge-transfer state expressed by (Al(4))(delta+)(NTCDA)(delta-). The binding of Al to NTCDA is strong. The C=O double-bond character of NTCDA is changed to C-O single-bond-like character by the strong interaction of Al to the C=O bond. This is the origin of the red-shift of the FT-IR spectrum. The electronic states of organic-inorganic hybrid material were discussed on the basis of theoretical results.     

Substituent effects on 13C-15N spin couplings and 13C chemical shifts in benzenediazonium ions

Similar trends are observed for ¹J(¹³C-¹⁵N) values for a series of aryldiazonium tetrafluoroborates and comparable anilinium fluorosulfonates. Contributions from resonance structures involving double-bond character in the CN bond are judged to be relatively unimportant in the ground state structure of aryldiazonium ions.     

Generalized anomeric interpretation of the "high-energy" N-P bond in N-methyl-N'-phosphorylguanidine: importance of reinforcing stereoelectronic effects in "high-energy" phosphoester bonds

Electronic structure calculations have been performed on a model N-phosphorylguanidine, or phosphagen, to understand the stereoelectronic factors contributing to the lability of the "high-energy" N-P bond. The lability of the N-P bond is central to the physiological role of phosphagens involving phosphoryl transfer reactions important in cellular energy buffering and metabolism. Eight protonated forms of N-methyl-N'-phosphorylguanidine have been energy minimized at levels of theory ranging up to B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) to investigate the correlation between protonation state and N-P bond length. Selected forms have also been minimized using the CCSD/6-311++G(d,p) and QCISD/6-311++G(d,p) levels of theory. Bulk solvation energies using the polarized continuum model (PCM) with B3LYP/6-311++G(d,p) test the influence of the surroundings on computed structures and energies. The N-P bond length depends on the overall protonation state where increased protonation at the phosphoryl group or deprotonation at the unsubstituted N' nitrogen results in shorter, stronger N-P bonds. Natural bond orbital analysis shows that the protonation state affects the N-P bond length by altering the magnitude of stabilizing n(O) --> sigma*(N-P) stereoelectronic interactions and to a lesser extent the sigma(N-P) --> sigma*(C-N') and sigma(N-P) --> sigma*(C-N) interactions. The computations do not provide evidence of a competition between the phosphoryl and guanidinium groups for the same lone pair on the bridging nitrogen, as previously suggested by opposing resonance theory. The computed n(O) --> sigma*(N-P) anomeric effect provides a novel explanation of "high-energy" N-P bond lability. This offers new mechanistic insight into phosphoryl transfer reactions involving both phosphagens and other biochemically important "high-energy" phosphoester bonds.     

Doubly bonded systems between heavier Group 15 elements

There has been much interest in the synthesis and properties of doubly bonded systems between heavier Group 15 elements, i. e. heavier analogues of azo-compounds (dipnictenes), from the viewpoints of fundamental and material chemistry. Although such double-bond compounds between heavier main group elements are known to be highly reactive, too much so to be isolated as stable compounds, a number of reports on the synthesis of kinetically stabilized diphosphenes (RP[double bond, length as m-dash]PR), diarsenes (RAs[double bond, length as m-dash]AsR), and phosphaarsenes (RP[double bond, length as m-dash]AsR) bearing bulky substituent have been published since 1980. We have also succeeded in the synthesis of the first stable distibene (RSb[double bond, length as m-dash]SbR) and dibismuthene (RBi[double bond, length as m-dash]BiR) by taking advantage of efficient steric protection groups, 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl (Tbt) and 2,6-bis[bis(trimethylsilyl)methyl]-4-[tris(trimethylsilyl)methyl]phenyl (Bbt), and revealed their structures and properties systematically. Thus, the doubly bonded compounds between heavier Group 15 elements are no longer imaginary species but are those with real existence which are stable, even in the case of the heaviest non-radioactive element bismuth, when they are appropriately protected by bulky substituents. This Perspective describes our research on the chemistry of kinetically stabilized double-bond compounds between heavier Group 15 elements.     

A theoretical study of the competitive homolytic/heterolytic aniomesolytic cleavages of C-O alkyl ether bonds

Density functional theory electronic structure calculations of the homolytic/heterolytic aniomesolytic C-O fragmentations in the gas phase of a series of radical anions of substituted-phenyl benzyl ethers and substituted-benzyl phenyl ethers have been carried out. Along the series, the electron-withdrawing strength of the substituents increases. An intramolecular electron transfer from the pi system to the sigma molecular orbital of the scissile C-O bond is required to produce the fragmentation. As the electron-withdrawing strength of the substituents increases, the transition-state structures appear later with higher potential energy and Gibbs free energy barriers. The homolytic mesolytic cleavages are always thermodynamically favored versus the corresponding heterolytic mesolytic ones. The heterolytic mesolytic fragmentations in radical anions containing only weak electron-withdrawing groups are faster than the corresponding homolytic mesolytic ones. Conversely, in radical anions supporting strong electron-withdrawing groups the homolytic mesolytic fragmentations are faster in terms of potential energy barriers. However, the entropic contribution makes it comparable the homolytic and the heterolytic Gibbs free energy barriers in this case. The main factors that determine the relative rates of those kind of aniomesolytic cleavages are discussed.     

Nucleophilic substitution reactions of 2,4,6-tris(trinitromethyl)-1,3,5-triazine. 2. interaction of 2,4,6-tris(trinitromethyl)-1,3,5-triazine with primary amines and hexamethyldisilazane

2-R-amino-4,6-bis (trinitromethyl)-1,3,5-triazines have been synthesized, and their structures have been established. Dynamic¹³C NMR spectroscopy has been used to measure the rotational barriers of the tertbutylamino group around the C₍₂₎-NHBu-t bond in 2-(tert-butylamino)-4,6-dichloro-1, 3, 5-triazine and 2-(tertbutylamino)-4,6-dimethoxy-1,3,5-triazine. X-ray diffraction was used to investigate the structure of 2-(tertbutylamino)-4,6-bis (trinitromethyl)-1,3,5-triazine. From the results obtained in this work it has been concluded that the bond between the NHBu-t group and the triazine ring has a partial double-bond character.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 117913. Translated from ] Khimiya Geterotsikiicheskikh Soedinenii, No. 5, pp. 679–688 May, 1995. Original article submitted March 7, 1995.     

Conformational analysis—CVI: On the 1,5-cyclooctadiene ring

1,5-cyclooctadiene and the corresponding dibenzo derivatives have been studied by means of force-field calculations. The relative stabilities of the various conformations, and the energy surfaces which interconnect them found from the calculations are used to interpret the available experimental data. Differences between the parent diene and the dibenzo derivative are noted, and are attributed largely to the difference in torsional barriers of a saturated carbon bond when attached to a double bond, as opposed to being attached to an aromatic ring.     

Molecular mechanics analysis of restricted rotation about pivot bond in substituted bicyclohexyls and phenylcyclohexanes. Importance of successive gauche and progauche sequences in conformational dynamics

Rotation of pivot bond in bicyclohexyls and phenylcyclohexanes carrying methyl groups vicinal to the rotating bond have been simulated by the second derivative molecular mechanics calculations. Barriers are characterized by long-range nonbonded interaction types occurring across the pivot bond such as gg, gp (p=progauche), po (o=ortho), ge (e=eclipse), ggg and gpo with alternating signs regarding gauche and progauche. Very high barriers are expected to appear when at least one 1,b interaction type, ggg or gpo, occurs simultaneously with another interaction type. Experimental examples including known atropisomers have been interpreted in the light of the present results.     

Electronic structure of the alpha and beta isomers of [Mo(8)O(26)](4-)

The structure and bonding in alpha and beta octamolybdate anions have been investigated using density functional methods. In general, good computational-experimental agreement for the geometrical parameters has been obtained. The electronic structure of the anions has been probed with molecular orbital and Mulliken-Mayer methods. All Mo-O interactions have been found to be predominantly d(Mo)-p(O) in character. Several multicentered molecular orbitals can be described as sigma or pi closed-loop structures, but the proposed connection with the stability of the polyanions is not completely supported by the calculations. Mayer indexes correspond to fractional multiple character for terminal bonds and approximately single or low-order character for bridging bonds, in accordance with structural and bond valence results. The valency analysis has yielded similar overall bonding capacity for the various oxygen atoms. A distribution of the negative charge over all types of oxygen sites and metal charges considerably smaller than the formal oxidation states have been obtained from the Mulliken analysis.     

A Generalized Unpaired Electron Spin Density Equation and Organic Hyperconjugation Mechanism

A large class of stereochemcial and related interactions in organic chemistry are repulsive and others are attractive, but the relative orientation of two methyl groups and the amount of energy required to twist one relative to the other (the hindered rotation energy barriers), or the alignment of such a group with respect to a conjugated ring to which it is attached (widely attributed to a mechanism called “hyperconjugation”) are estimated to be small in compared with the total energy of the molecule. We used theories of both isotropic and anisotropic proton hyperfine interactions in the π‐electron systems developed in the early sixties. They are approximated by the magnetic dipole nteractions between each proton and an electron spin magnetization that is distributed in 2s and 2p Slater atomic orbitals center on carbon atoms. We have extended these theories to the non‐planar olefinic cation radicals, which are very important in biochemistry as well as in petroleum catalysis. A three dimensional electron spin density equation has been developed in this paper to handle some Jahn‐Teller vibronic molecules. The new electron spin density equation related the observed proton hyperfine splittings to the non‐planar structures of the open‐chain alkene cation radicals generated by radiolysis and various chemical oxidation methods. The spin densities and the conformational calculations based on valence bond theory and symmetry principles are compared with some more elaborated molecular orbital calculations in the literature. The localized valence bond approaches are better in accord with our experimental results. The anomalous line‐width effect of the four methyl groups observed in the 2,3‐dimethyl‐2‐butene cation radicals also confirmed the positive sign of the electron‐proton hyperfine constant of hyper‐conjugation mechanism. A methyl substituent attached to a conjugated molecule often behaves as if it formed part of the region of conjugation; the charge appears to flow from the methyl group into the π electron system and it may also give rise to an appreciable dipole moment. Methylation also gives rise to an appreciable dipole moment, and the resultant red shift of electronic absorption bands is of some importance in the design of dye molecules.     

Protonation of 5‐methylhydantoin and its thio derivatives in the gas phase: A theoretical study

The gas phase proton affinities of 5‐methylhydantoin and its thio derivatives were theoretically studied through the use of high‐level density functional theory calculations. The structure of all possible tautomers and their conformers were optimized at the B3LYP/6‐311+(d,p) level of theory. Final energies were obtained at the B3LYP/6‐311+(2df,2p) level. The imidazolidone derivatives 5‐methyl‐2,4‐dioxo imidazolidine, 5‐methyl‐2‐oxo‐4‐thio imidazolidine, 5‐methyl‐2‐thio‐4‐oxo imidazolidine, and 5‐methyl‐2,4‐dithio imidazolidine possess moderately strong proton affinities. Protonation at sulfur would be larger than protonation at oxygen. The most stable protonated forms of 2O4O and 2S4O have the proton attached to the heteroatom in position 2, whereas protonation of 2O4S and 2S4S preferentially takes place at position 4. The barriers for proton migration between the different tautomers are rather large. The energy decomposition analysis analysis of the O? H⁺ and S? H⁺ interactions suggests that the bonding interactions come mainly from the covalent bond formation. The contribution of the Coulomb attraction is rather small. © 2012 Wiley Periodicals, Inc.     

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.     

Probing the photochemical mechanism in photoactive yellow protein

Selectively bridged model compounds related to the chromophore in photoactive yellow protein have been synthesized where the single bond adjacent to the benzene ring (bond 1) and where both bond 1 and the adjacent double bond (bond 2) are bridged. They were compared to the nonbridged reference compound regarding their photophysical properties using steady-state and time-resolved fluorescence at various temperatures. Quantum chemical calculations were additionally performed and showed that several conformers are populated in the ground state. The neutral model compounds show that the nonradiative deactivation channel is linked to both single- and double-bond twisting. The relative importance of single-bond twisting is increased for the corresponding deprotonated hydroxy compounds with an enhanced donor character. The simultaneous photochemical activity of both single and double bonds explains the ease of photochemical isomerization in the confined environment of the natural PYP protein and also of the primary step in the vision process in rhodopsin.     

Conformation, Inversion Barrier, and Solvent-Induced Conformational Shift in Exo- and Endo/Exo-Calix[4]arenes

Calixarenes 4a and 4b having hydroxyl groups in endo and exo positions and the ethanediyl-bridged exo-calixarene 5a were synthesized by a stepwise strategy. Single-crystal X-ray structures were obtained for 4a and for the exo-calixarene 3d, showing the molecules to exist in the 1,2-alternate conformation which is also found for 4a,b in solution. The inversion barriers of 4a and 4b (10.3 and 10.8 kcal mol(-1)) are similar to that determined for the endo-dihydroxycalixarene 12, indicating that the additional intramolecular hydrogen bond between the exo OH groups does not decrease the flexibility of the molecule. In CDCl(3) solution exo-calixarene 5a adopts a 1,2-alternate conformation with the methyl group at the bridge located in an axial position, while in DMSO-d(6) the conformation adopted is the partial cone. Similar solvent-induced conformational shifts were found for the exo-calixarenes 3b and 3d. MM3 calculations predict that the cone form is the lowest energy conformation of 4 and the exo-calixarenes 3 and 5. The calculations suggest that the conformational preferences of the methyl group at the bridge for either the axial or equatorial positions are in large part determined by the repulsive steric interactions with the hydroxyl groups. The inversion barrier of 4b is satisfactorily reproduced by calculations, which indicate that the rotation of the exo rings is less energetically demanding than the rotation of the endo rings.     

PHOTOCHEMISTRY OF BIOLOGICAL MOLECULES – II. PHOTOLYSIS OF DIPEPTIDES IN THE SOLID STATE

Abstract— Photolysis with light of 2537 Å of a series of aliphatic dipeptides in the solid state has been shown to lead to bond rupture and free radical formation. The structures of the radicals have been determined by ESR techniques and in general, the free electron has been shown to reside on the carbon atom attached to the nitrogen atom of the peptide bond. Dipeptides containing phenylalanine residues show ESR spectra typical of the free amino-acid in the terminal position.     

Hydrogen Bonds of Peptide Group in Four Acetamide Derivatives: DFT Study of Oxygen and Nitrogen NQR and NMR Parameters

A computational study was conducted to examine hydrogen bond (HB) properties of peptide group in four derivatives of acetamide by density functional theory (DFT) calculations of nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) parameters at the sites of oxygen and nitrogen nuclei of peptide groups. The available crystalline structures of four derivatives; 2,2,2-trifluoro-N-(2-hydroxy-5-nitrophenyl)acetamide, N-(2-acetylphenyl)acetamide, 2-chloro-N-(4-nitrophenyl) acetamide, and N-(4-fluorophenyl)acetamide were obtained from literature. Following the influence of HB interactions, calculations were done on non-hydrogen bonded (single) and hydrogen bonded (cluster) models of derivatives. The results revealed different behaviors of peptide group in contributing to HB interactions in different derivative structures. HB interactions are the strongest in 2-chloro-N-(4-nitrophenyl)acetamide. However, the strengths of HB interactions in all of the four derivatives are still less than that of acetamide. The calculations are done at the level of B3LYP method and 6-311++G** standard basis set using GAUSSIAN 98 package of program.     

Molecular modeling studies of novel heteroarotinoids

The molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles ?₁ and ?₂ in closest agreement with the crystal structure, and all three computational methods yield values of ?₁ and ?₂ within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus ?₁ and ?₂ indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.     

Ab initio studies of push–pull systems

Twelve push–pull ethylene derivatives, NH₂CH=CHX, NH₂C≡CCH=CHX, and ⁻OCHX=CHX (with X=BH₂, C≡N, NO₂, and CH₂ ⁺) have been studied by ab initio calculations. The rotational barrier around the central double bond was chosen as a probe for push–pull effects, as push–pull effects would remove electron density from the central double bond. The amount of reduction of double bond character will increase with the contribution of the zwitterionic resonance hybrid structure. Complete geometry optimizations and calculations of vibrational frequencies were performed for all minima and transition state structures of these 12 systems. The calculations were carried out with the B3LYP and MP2 methods using the 6-311+G(d,p) and the 6-311++G(d,p) basis sets. All the systems investigated exhibited properties consistent with push–pull effects such as elongated C=C double bonds, dipolar electronic structures, and reduced barriers to internal rotation.