Pentagon Stability in Cycloarsanes

The orbital phase theory leads to the prediction that the saturated arsenic cyclic molecules prefer pentagons, which is substantiated by the negative strain energy of cyclic As 5 H 5 . The puckered five-membered arsenic ring is an important structural unit for the pentagon stability. Possible structures and conformers of polycycloarsanes As 8 H 4 , As 11 H 3 , "roof-like" and "cage-like" As 12 H 4 , As 13 H 3 , As 14 H 2 , and As 15 H 3 with relatively low strain energies were predicted due to many puckered pentagon units in them. The low stability of the dodecahedron As 20 with 12 planar pentagon units was suggested by the high strain energy.     

Thermochemistry of N‐heterocyclic carbenes with 5‐, 4‐, 3‐, and 2‐membered rings

N‐heterocyclic carbenes (NHCs) based on imidazole‐2‐ylidene ( 1 ) or the saturated imidazolidine‐2‐ylidene ( 2 ) scaffolds are long‐lived singlet carbenes. Both benefit from inductive stabilization of the sigma lone pair on carbon by neighboring N atoms and delocalization of the N pi lone pairs into the nominally vacant p‐pi atomic orbital at the carbene carbon. With thermochemical schemes G4 and CBS‐QB3, we estimate the relative thermodynamic stabilization of smaller ring carbenes and acyclic species which may share the keys to NHC stability. These include four‐membered ring systems incorporating the carbene center, two trivalent N centers, and either a boron or a phosphorus atom to complete the ring. Amino‐substituted cyclopropenylidenes have been reported but three‐membered rings containing the carbene center and two N atoms are not known. Our calculations suggest that amino‐substituted cyclopropenylidenes are comparable in stability to the four‐membered NHCs but that diazacyclopropanylidenes would be substantially less effectively stabilized. Concluding the series are acyclic carbenes with and without neighboring N atoms and a series of “two‐membered ring” azapropadienenylidene cations of form :C?N?W with W = an electron‐withdrawing agent. We have studied W = NO₂, CH₂(+), CF₂(+), and (CN)₂C(+). Although these systems display a degree of stabilization and carbene‐like electronic structure, the stability of the NHCs is unsurpassed. © 2014 Wiley Periodicals, Inc.     

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C−N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a–2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C−N), which is why the six-membered ring lactams C−N bond are more rigid than those with five-membered ring lactams. The calculated ΔG^# values from the acylation reaction of the lactams (involving the S−H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C−N cleavage in the five-membered ring lactams especially in the 1–2 derivatives (17.58 kcal mol⁻¹). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.     

Strain energies due to nonplanar distortion of fullerenes and their dependence on structural motifs

Accurate strain energies due to nonplanar distortion of 114 isolated pentagon rule (IPR) fullerenes with 60-102 carbon atoms have been calculated based on B3LYP/6-31G(d) optimized structures. The calculated values of strain energy due to nonplanar distortion (Enp) are reproduced by three simple schemes based upon counts of 8, 16, and 30 distinct structural motifs composed of hexagons and pentagons. Using C180 (Ih) and CN (Ih) (N is very large) as test molecules, the intrinsic limitations of the motif model based on six-membered rings (6-MRs) as the central unit have been discussed. On the basis of the relationship between the contributions of motifs to Enp and the number of five-membered rings (5-MRs) in motifs, we found that IPR fullerenes with dispersed 5-MRs present smaller nonplanar distortions.     

A theoretical and structural investigation of thiocarbon anions

Density functional theory energies, geometries, and population analyses as well as nucleus-independent chemical shifts (NICS) have been used to investigate the structural and magnetic evidence for cyclic CnSn(2-) and CnSn (n = 3-6) electron delocalization. Localized molecular orbital contributions to NICS, computed by the individual gauge for localized orbitals method, dissect pi effects from the sigma single bonds and lone pair influences. CnSn(2-) (n = 3-5) structures in Dnh symmetry are minima. Their aromaticity decreases with increasing ring size. C3S3(2-) is both sigma and pi aromatic, while C4S4(2-) and C5S5(2-) are much less aromatic. NICS(0)pi, the C-C(pi) contribution to NICS(0) (i.e., at the ring center), decreases gradually with ring size. In contrast, cyclic C6S6(2-) prefers D2h symmetry due to the balance between aromaticity, strain energy, and the S-S bond energies and is as aromatic as benzene. The theoretical prediction that C6S6(6-) has D6h minima was confirmed by X-ray structure analysis. Comparisons between thiocarbons and oxocarbons based on dissected NICS analysis show that CnSn(2-) (n = 3-5) and C6S6(6-) are less aromatic in Dnh symmetry than their oxocarbon analogues.     

Thermodynamic analysis of strain in the five-membered oxygen and nitrogen heterocyclic compounds

Cyclopentane is conventionally strained. Replacement of a carbon atom by a heteroatom obviously impacts angular strain in the five-membered ring compounds. Changes of strains in the five-membered cycles are also caused by a double bond or atttached benzene rings. We studied the thermochemical properties of Indane, 2,3-dihydrobenzofuran, indoline, N-methyl-indoline, carbazole, and N-ethyl-carbazole to obtain a better quantitative understanding of the energetics associated with these compounds containing five-membered ring units. We used combustion calorimetry, transpiration method, and high-level first-principles calculations to derive gaseous enthalpies of formation of the five-membered heterocyclic compounds. Our new values together with the selected values for parent heterocyclic compounds, available from the literature, were used for calculation of the strain energies H(S) of five-membered C-, N-, and O-containing cycles. Quantitative analysis of the resulting stabilization or destabilization of a molecule due to interaction of benzene rings with the heteroatom has been performed.     

Cooperative effects and strengths of hydrogen bonds in open-chain cis-triaziridine clusters (n = 2-8): a DFT investigation

We employ DFT/B3LYP method to investigate linear open-chain clusters (n = 2-8) of the cis-triaziridine molecule that is a candidate molecule for high energy density materials (HEDM). Our calculations indicate that the pervasive phenomena of cooperative effects are observed in the clusters of n = 3-8, which are reflected in changes in lengths of N...H hydrogen bonds, stretching frequencies, and intensities of N-H bonds, dipole moments, and charge transfers as cluster size increases. The n(N) --> sigma*(N-H) interactions, i.e., the charge transfers from lone pairs (n(N)) of the N atoms into antibonds (sigma*) of the N-H bonds acting as H-donors, can be used to explain the observed cooperative phenomena. The approaches based upon natural bond orbital (NBO) method and theory of atoms in molecule (AIM) to evaluating N...H strengths are found to be equivalent. In the process of N...H bonding, cooperative nature of n(N) --> sigma*(N-H) interactions promotes formation of stronger N...H bonds as reflected in increases in the capacities of cis-triaziridine clusters to concentrate electrons at the bond critical points of N...H bonds. The calculated nonadditive energies also show that the cooperative effects due to n(N) --> sigma*(N-H) interactions indeed provide additional stabilities for the clusters.     

An orbital phase theory for the torquoselectivity of the ring-opening reactions of 3-substituted cyclobutenes: geminal bond participation

We apply an orbital phase theory to the torquoselectivity of the electrocyclic reactions of 3-substituted (X) cyclobutenes. The torquoselectivity is shown to be controlled by the orbital-phase relation of the reacting pi(CC) and sigma(CC) bonds with the sigma(CX) bond geminal to the sigma(CC) bond to be cleaved. The inward rotation of electron-donating sigma(CX) bonds and outward rotation of electron-withdrawing sigma(CX) bonds have been deduced from the orbital-phase theory. Enhancement of the inward rotation by the electron-donating capability of the sigma(CX) bonds is confirmed by the correlation between the torquoselectivity and sigma(CX) orbital energy. The orbital overlaps between the geminal sigma(CX) (sigma(CH)) and sigma(CC) bonds are found to be important as well. Unsaturated substituents with low-lying unoccupied pi orbitals also promote the inward rotation.     

Downfield proton chemical shifts are not reliable aromaticity indicators

[structure: see text] The downfield chemical shifts of arene hydrogens (delta (1)H) are due only in part to the pi ring current contribution [sigma(//)(pi)]; local framework effects are equally important. Neither proton chemical shifts nor even sigma(||)(pi) tensor elements, per se, are reliable aromaticity indicators. Unsaturated polycyclic hydrocarbons with nonaromatic quinoid structures have delta (1)H and sigma(//)(pi) values in the "aromatic range". Conversely, numerous aromatic protons, including those in five-membered ring heterocycles, resonate in the "nonaromatic range".     

Thermodynamic analysis of strain in heteroatom derivatives of indene

Thermochemical properties of indene, 2,3-benzofuran, indole, and N-methylindole have been studied to obtain a better quantitative understanding of the energetics associated with these compounds containing five-membered ring units. We used combustion calorimetry, transpiration, and high-level first-principles calculations to derive gaseous enthalpies of formation of the five-membered heterocyclic compounds. Our new values together with selected values for the parent heterocyclic compounds, available from the literature were used for calculation of the strain enthalpies H(S) of five-membered C, N, and O-containing cycles. The quantitative analysis of the resulting stabilization or destabilization of a molecule due to interaction of the benzene ring with the heteroatom has been performed.     

How electron delocalization influences the electron-withdrawing properties of isomeric benzobischalcogenadiazoles

The fermionic potential and delocalization indices for benzo-bis-1,2,5-chalcogenadiazoles reveal inhomogeneous electron delocalization in their benzene ring, which results in compactly localized lone electron pairs on the chalcogen atoms. These features of (de)localization are rooted in a local increase in the kinetic component of the electron correlation, which expresses the Fermi hole variability and the kinetic potential response to electron density variations in the benzene ring of benzobis-1,2,5-chalcogenadiazoles. This explains their better electron-withdrawing properties compared to benzobis-1,2,3-chalcogenadiazoles     

C20三个异构体稳定性的从头计算研究

采用HF,B3LYP,MP2和QCISD等理论方法在6-31G和6-31G^*基组水平上,对C20的3个主要异构体碟型(Bowl)、笼型(Cage)和环型(Ring)的结构进行理论研究,得出这3个异构体的相对稳定性的次序为:Ring>Bowl>Cage.计算结果显示,分子轨道具有离域特性,电子的这种离域特征有利于原子间更好的成键,可避免出现大的张力,这是Cage型异构体虽然违反“五元环隔离规则”(Isolatedpentagonrule)却能稳定存在的原因.     

二(乙二胺)(2-氨基乙基)合钴(III)配合物构象研究

本文利用CFF方法分析了Co(Ⅲ)配合物二齿配体中较少见的四员环构象的特征,并模拟了这个四员环在配位环境下构象变化的过程。标题配合物[Co(CH_2CH_2NH_2)(NH_2CH_2CH_2NH_2)_2]~(2+)(图1)为光化学反应的中间产物,     

Investigations of coupling characters in ionic liquids formed between the 1-ethyl-3-methylimidazolium cation and the glycine anion

In this study, novel ionic liquids formed between the 1-ethyl-3-methylimidazolium cation [emim]+ and the glycine anion [Gly]- have been investigated theoretically. The relevant geometrical characteristics, energy properties, the characters of the intermolecular hydrogen bonds (H bonds), and the possibility of proton transfer as well as IR characteristics have been systematically discussed. The natural bond orbital (NBO) and atoms in molecule (AIM) analyses have also been applied to understand the nature of the interactions between ionic pairs in ionic liquids. The most stable geometries have been determined by analyzing the relative energies and interaction energies, where the C-H...O intermolecular H bonds involving the protons attached to the imidazolium ring have been found to possess partial covalent character in nature. Electron transfers from the lone pairs of the carbonyl O atom of [Gly]- to the C-H antibonding orbital of the [emim]+ can explain the elongation and red shift of the C-H stretching frequency. The interaction modes are more favorable when the carbonyl O atoms of [Gly]- interact with the C2-H of the imidazolium ring and the C-H of the methyl group through the formation of double H bonds. The origin of the high stability of the amino acid ionic liquids observed experimentally may be attributed to the nonexistence of the proton-transferred products (neutral pairs) together with the large energy needed for separation of the ionic pairs. Additionally, the characteristics of the IR spectra have been analyzed to demonstrate the variants of the molecular structure of the [emim]+[Gly]- ionic liquids.     

Theoretical investigation of next neighbour interactions and ring strain in linear and monocyclic phosphanes

The molecules PH₃, P₂H₄, P₃H₅, P₃H₃, P₄H₄, and P₅H₅ were treated at the SCF level using basis sets of DZP quality. Computed structure constants and energies indicate high stability for P₅-ring systems and small ring strain for P₃- and P₄-ring systems. The computed values for the strain are 28 and 18 kJ/mol for P₃H₃ and P₄H₄, respectively. Neighbouring P atoms with transconfigured lone pairs are favoured in the monocyclic phosphanes considered in this work, as shown by the energy difference of about 10 kJ/mol between trans and cis configured lone pairs, and the shortening of P-P distances by about 2 pm for trans configured P atoms.     

Trans-hydrogen-bond (h2)J(NN) and (h1)J(NH) couplings in the DNA A-T base pair: natural bond orbital analysis

Natural bond orbital (NBO) analysis described here demonstrates that trans-hydrogen-bond (trans-H-bond) NMR J couplings in the DNA A-T base pair, h2JNN and h1JNH, are determined largely by three terms: two Lewis-type contributions (the single-orbital contribution from the adenine lone pair and the contribution from the sigmaN3H3 natural bond orbital of the thymine ring) and one contribution from pairwise delocalization of spin density (between the lone pair in adenine and the sigma* antibonding orbital linking N3 and H3 of thymine). For h2JNN coupling, all three contributions are positive, whereas for h1JNH coupling, the delocalization term is negative, and the other two terms are positive, resulting in a small net positive coupling constant. This result rationalizes the experimental findings that the two-bond coupling (h2JNN approximately 9 Hz) is larger than the one-bond coupling (h1JNH approximately 3 Hz) and demonstrates that the same hyperconjugative and steric mechanisms that stabilize the H-bond are involved in the transmission of J coupling information. The N1...H3-N3 H-bond of the DNA A-T base pair is found to exhibit significant covalent character, but steric effects contribute almost equally to the trans-H-bond coupling.     

Are oxocarbon dianions aromatic?

Assessment of the cyclic electron delocalization of the oxocarbon dianions, C(n)()O(n)()(2)(-) and their neutral counterparts C(n)()O(n)() (n = 3-6), by means of structural, energetic, and magnetic criteria, shows that C(3)O(3)(2)(-) is doubly aromatic (both sigma and pi cyclic electron delocalization), C(4)O(4)(2)(-) is moderately aromatic, but C(5)O(5)(2)(-), as well as C(6)O(6)(2)(-), are less so. Localized orbital contributions, computed by the individual gauge for localized orbitals method (IGLO), to the nucleus-independent chemical shifts (NICS) allow pi effects to be disected from the sigma single bonds and other influences. The C-C(pi) contribution to (NICS(0,pi) (i.e., at the center of the ring) in oxocarbon dianions decreases with ring size but shows little ring size effect at points 1.0 A above the ring. On the basis of the same criteria, C(4)O(4) exhibits cyclic electron delocalization due to partial occupancy of the sigma CC bonds. However, the dissociation energies of all the neutral oxocarbons, C(n)()O(n)(), are highly exothermic.     

Influence of calculation level and effect of methylation on axial/equatorial equilibria in piperidines

A detailed conformational analysis was performed on the chair forms of piperidine, N-methylpiperidine, and some methylated derivatives using Hartree–Fock (HF) and MP2 ab initio methods with several basis sets (from 3–21G to 6–311++G**), and the most widely used semiempirical approaches (MNDO, AM1, and PM3). It was found that the use of polarized basis sets at the HF level is adequate enough for the prediction of conformational preferences in the axial/equatorial equilibrium of the N-R group in piperidines. On the other hand, the inclusion of electron correlation becomes necessary for predicting the axial/equatorial energy differences of the equilibria of the methyl group. Semiempirical methods are not recommended, because AM1 and PM3 predict opposite stabilities to those obtained experimentally and MNDO ring geometries are systematically too flat. The origin of the conformational stabilities was interpreted in terms of the natural bond orbital analysis of the HF/6–31G** wave functions. The equatorial preferences in the N-H equilibria is mainly due to lower Lewis energies, although delocalization of the nitrogen lone pair is favored in N-H axial forms. N-Methylation increases the equatorial M-Me preferences, because the Lewis energy of axial N-Me forms increases due to larger 1,3-diaxial interactions. Geometrical trends associated with the delocalization of the nitrogen lone pair and with interactions between the introduced N-R and C-Me groups were discussed and related to the degree of planarity of the six-membered ring by means of the puckering coordinates defined by Pople and Cremer. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 961–976, 1998     

Structural and spectroscopic properties of trans-difluoro(1,4,8,12-tetraazacyclopentadecane)chromium(III) perchlorate hydrate

The structure of [CrF(2)([15]aneN(4))]ClO(4).H(2)O ([15]aneN(4)=1,4,8,12-tetraazacyclopentadecane) has been determined by a single-crystal X-ray diffraction study at 173 K. The complex crystallizes in the space group P1- of the triclinic system with two mononuclear formula units in a cell of dimensions a=9.6117(7) A, b=10.2882(7) A, c=11.0001(7) A and alpha=99.7570(10) degrees, beta=105.6080(10) degrees and gamma=113.7130(10) degrees. The complex cation unit has its central Cr atom in an octahedral coordination with four nitrogen atoms and two fluorine atoms in a trans position. Three six-membered and one five-membered chelate rings of the [15]aneN(4) ligand are in a chair-twist(skew)-chair-gauche conformation sequence. The gauche five-membered ring is disordered with the twist six-membered ring opposite. The four H atoms in the chiral N atoms have the trans-II (CTCg) type configuration. The mean Cr-N and Cr-F bonds are 2.095(2) and 1.8752(13) A, respectively. The IR and visible spectral properties are consistent with the result of X-ray crystallography. The resolved band maxima of the electronic d-d spectrum are fitted with secular determinant for quartet state energy of d(3) configuration in tetragonal field including configurational but neglecting spin-orbit coupling. It is confirmed that the fluoride has strong sigma- and pi-donor properties toward the chromium(III) ion and the nitrogen atoms of the [15]aneN(4) ligand also have a strong sigma-donor character.     

Anomeric effect in "high energy" phosphate bonds. Selective destabilization of the scissile bond and modulation of the exothermicity of hydrolysis

A natural bonding orbital (NBO) analysis of phosphate bonding and connection to experimental phosphotransfer potential is presented. Density functional calculations with the 6-311++G(d,p) basis set carried out on 10 model phosphoryl compounds verify that the wide variability of experimental standard free energies of hydrolysis (a phosphotransfer potential benchmark) is correlated with the instability of the scissile O-P bond through computed bond lengths. NBO analysis is used to analyze all delocalization interactions contributing to O-P bond weakening. Phosphoryl bond lengths are found to correlate strongest (R = 0.90) with the magnitude of the ground-state n(O) --> sigma*(O-P) anomeric effect. Electron-withdrawing interactions of the substituent upon the sigma(O-P) bonding orbital also correlate strongly with O-P bond lengths (R = 0.88). However, an analysis of sigma*(O-P) and sigma(O-P) populations show that the increase in sigma*(O-P) density is up to 6.5 times greater than the decrease in sigma(O-P) density. Consequently, the anomeric effect is more important than other delocalization interactions in impacting O-P bond lengths. Factors reducing anomeric power by diminishing either lone pair donor ability (solvent) or antibonding acceptor ability (substituent) are shown to result in shorter O-P bond lengths. The trends shown in this work suggest that the generalized anomeric effect provides a simple explanation for relating the sensitivity of the O-P bond to diverse environmental and substituent factors. The anomeric n(O) --> sigma*(O-P) interaction is also shown to correlate strongly with experimentally determined standard free energies of hydrolysis (R = -0.93). A causal mechanism cannot be inferred from correlation. Equally, a P-value of 1.2 x 10(-4) from an F-test indicates that it is unlikely that the ground-state anomeric effect and standard free energies of hydrolysis are coincidentally related. It is found that as the exothermicity of hydrolysis increases, the energy stabilization of the ground-state anomeric effect increases with selective destabilization of the high-energy O-P bond to be broken in hydrolysis. The anomeric effect therefore partially counteracts a larger resonance stabilization of products that makes hydrolysis exothermic and needs to be considered in achieving improved agreement between calculated and empirical energies of hydrolysis. The avenues relating the thermodynamic behavior of phosphates to underlying structural factors via the anomeric effect are discussed.