Bader's AIM Research Articles

Two Modifications Formed by “Sulflower” C16S8Molecules, Their Study by XRD and Optical Spectroscopy (Raman, IR, UV−Vis) Methods

Sublimation of sulflower, octathio[8]circulene C 16S 8 ( 1), on heating under high vacuum ( approximately 10 (-5) Torr) leads to successive formation of two modifications: a white film ( 1W) and a red polycrystalline solid ( 1R). When kept at room temperature for several weeks, 1W spontaneously turns pink, reflecting the monotropic phase transition 1W --> 1R. The accurate molecular and crystal structure of 1R has been studied using low-temperature (100 K) high-resolution single crystal X-ray analysis. The C 16S 8 molecule in crystal is strictly planar with nearly equalized bonds of each type (C-C, C-S, and CC). The point symmetry group of the free molecule is D 8 h , and the crystal space group is P2 1/ n. These data allowed group-theoretical analysis of vibrational normal modes to be accomplished. Investigation of the charge density distribution of 1R including Bader's AIM approach has revealed rather strong intermolecular S...S, S...C, and C...C interactions of charge transfer and pi-stacking types with overall lattice energy of 28.5 kcal/mol. The charge transfer due to the S...S interactions is the reason for the red coloration of 1R. The latter is reflected by its UV-vis spectrum exhibiting absorption bands in the visible region which are absent from that of 1W. Both modifications were studied comparatively by vibrational (Raman, IR) and electronic spectroscopies as well as XRD powder diffraction. All the results obtained are fully consistent and show that 1W is much less ordered than 1R with significantly weakened intermolecular interactions. Rationalizing of these results has led to an idea that 1W could be soluble, in contrast to 1R. Indeed, 1W appeared soluble in common solvents; this finding opens the way to the study of the chemistry of 1 and investigation of its electrooptical properties.

Relationship between substituent effect and aromaticity – Part III: naphthalene as a transmitting moiety for substituent effect

AbstractMolecular geometry of 10 isomeric nitronaphtholate ions (excludingperi‐ andortho‐type substituted systems), 1‐ and 2‐naphtholate ions, 1‐ and 2‐nitronaphthalene,meta‐ andpara‐nitrophenolate, phenolate, and nitrobenzene were optimized at B3LYP/6‐311G** level of approximation. Substituent effect stabilization energy (SESE), geometry‐based aromaticity index HOMA, magnetism‐based indices NICS, NICS(1), NICS(1)zz, and parameters characterizing Bond Critical Points (BCP) (ρ, ▿2ρ, ellipticity, ion/cov) of the Bader AIM theory were used to characterize transmitting properties for substituent effect through the naphthalene moiety. It results from our study that the studied systems could be clearly divided into two groups, (i) apara‐type group, where the intramolecular charge transfer between theπ‐electron donating andπ‐electron accepting substituents can be described by canonical forms with charge separation (as in the case ofpara‐nitrophenolate) and (ii) ameta‐type group, where this transfer requires using canonical forms with double charge separation (as in the case ofmeta‐nitrophenolate). Copyright © 2007 John Wiley & Sons, Ltd.

Bond Orders and Atomic Properties of the Highly Deformed Halogenated Fullerenes C60F18 and C60Cl30 Derived from their Charge Densities

The experimental charge densities of the halogenated C(60) fullerenes C(60)F(18) and C(60)Cl(30) were determined from high-resolution X-ray data sets measured with conventional Mo(Kalpha) radiation at 20 K for C(60)Cl(30) and with synchrotron radiation at 92 K for the fluorine compound. Bond topological and atomic properties were analyzed by using Bader's AIM theory. For the different C--C bonds, which vary in lengths between 1.35 and 1.70 A bond orders n between n=2 and significantly below n=1 were calculated from the bond topological properties at the bond critical points (BCP's). The low bond orders are seen for 5/6 bonds with each contributing carbon carrying a halogen atom. By integration over Bader's zero flux basins in the electron density gradient vector field atomic properties were also obtained. In contrast to free C(60), in which all carbon atoms have a uniform volume of 11 A(3) and zero charge, atomic volumes vary roughly between 5 and 10 A(3) in the halogenated compounds. Almost zero atomic charges are also found in the Cl derivative but a charge separation up to +/-0.8 e exists between C and F in C(60)F(18) due to the higher fluorine electronegativity, which is also seen in the electrostatic potential for which the electronegativity difference between carbon and fluorine, and the addition to one hemisphere of the fullerene cage leads to a strong potential gradient along the C(60)F(18) molecule. From the summation over all atomic volumes it follows that the halogen addition does not only lead to a dramatic distortion of the C(60) cage but also to a significant shrinkage of its volume.

The metal-rich palladium chalcogenides Pd 2MCh2 ( M=Fe, Co, Ni; Ch=Se, Te): Crystal structure and topology of the electron density

Crystals of Pd 2 MCh 2 ( M=Fe, Co, Ni; Ch=Se, Te) were synthesized by heating the elements at 823–1323 K in silica ampoules under argon atmosphere. Their structures were determined by single-crystal X-ray diffraction at room temperature. The metallic compounds crystallize in a variant of the K 2ZnO 2 type ( Ibam, Z=4, Pd 2CoSe 2: a=5.993(1), b=10.493(2), c=5.003(1) Å; Pd 2FeSe 2: a=5.960(1), b=10.576(2), c=5.078(1) Å; Pd 2CoTe 2: a=6.305(1), b=11.100(2), c=5.234(1) Å; Pd 2NiTe 2: a=6.286(1), b=11.194(2), c=5.157(1) Å). One-dimensional ∞ 1 [ MC h 4 / 2 ] tetrahedra chains with remarkably short M— M bonds run along [001], separated by [Pd 2] dumbbells with palladium in fivefold coordination of selenium or tellurium atoms. The structure may also be described as a filled variant of the SiS 2 type. M atoms occupy 1 4 of the tetrahedral voids and the Pd atoms fill all octahedral voids in a distorted ccp motif of chalcogen atoms. Even though the Pd 2 MCh 2 compounds are isotypic to K 2ZnO 2 from the crystallographic viewpoint, we find a different bonding situation with additional homo- and heteronuclear metal–metal bonds between the Pd and Co atoms. The electronic structures and topologies of the electron densities of Pd 2CoSe 2 and isotypic Na 2CoSe 2 are analyzed and compared by using Bader's AIM theory. Different values of topological charge transfer and electron density flatness indices uncover striking quantitative differences in the nature of chemical bonding between the metallic compound Pd 2CoSe 2 and nonmetallic Na 2CoSe 2.

Strikingly Long C···C Distances in 1,2-Disubstitutedortho-Carboranes and Their Dianions

Neutral and especially dianionic 6- and 12-vertex closo ortho-carboranes (o-carboranes) 1,2-R2-1,2-C2BnHn (R = H, CH3, NH2, OH, F, SiH3, PH2, SH, Cl, as well as e-, CH2-, NH-, O-, SiH2-, PH-, and S- exhibit extremely large variations (over 1 A!) of the cage CC distances, from 1.626 to 2.638 A, at the B3LYP/6-31G//B3LYP/6-31G DFT level. These CC "bond lengths," among the longest ever reported, generally are greater in the icosahedral than those in the corresponding octahedral systems and depend strongly on the substituents. While 1,2-(NH2)2-1,2-C2B10H10 has the longest Cc...Cc separation in neutral species (1.860 A), Cc...Cc distances can be much larger in the corresponding dianions. These range from 1.823 A (R- = e-) to 2.638 A (R- = CH2-) for 1,2-(R-)2-1,2-C2B10H10 and from 1.626 A (R- = SiH2-) to 3.099 A (R- = NH-) for 1,2-(R-)2-1,2-C2B4H4. Remarkably, there is no abrupt discontinuity over the entire range of CC lengths. Consequently, the relationship between the gradual changes in the distances and the nature of the bonding was analyzed by means of the form of the Kohn-Sham orbitals, the Wiberg Cc...Cc bond indices, and Bader AIM method. Cluster carboranes, and possibly other heteroboranes, thus appear to offer unique opportunities for modulating Cc...Cc distances.

Close shell interactions in 3-ethoxycarbonyl-4-hydroxy-6-methoxymethyleneoxy-1-methyl-2-quinolone: 100 K single crystal neutron diffraction study and ab initio calculations

The molecular and crystal structures of the title compound have been determined from a single crystal neutron diffraction experiment at 100 K. A comparison between the main geometrical features and related properties of the in-crystal and the ab initio optimized free molecule structures has shown that crystal packing induces a significant distortion in the molecular geometry. Packing instead would only have a moderate effect on the observed intramolecular resonance assisted hydrogen bond. Supermolecular ab initio molecular orbital calculations have been performed on the six different dimers one molecule forms with its nine nearest neighbours. The obtained results clearly show that dispersion contributions dominate in the most strongly interacting dimers, in good qualitative accord with the predictions made by using different empirical potentials. A qualitative description of the most prominent inductive effects determined from the electron density deformation upon dimer formation is presented. Topological analyses of the dimers charge densities have been performed in the framework of the Bader's AIM theory and all the intermolecular bond critical points have been identified. An attempt to determine some of the interaction energies only from topological quantities made evident the practical limitations of such an approach.

Properties of a new fluorescent coumarin derivatization reagent employing molecular modelling techniques

Coumarins are widely employed in chemical analysis due to their fluorescent properties. The conformation and the electronic properties of a newly synthesized derivatization reagent namely BrMOZPhC (4-bromomethyl-coumarin-7-phenyl[6,7-b](9,6)oxazine) was studied. The molecule was found to possess completely planar structure, which enhances the fluorescent quantum yield. Furthermore it exhibits a high degree of aromaticity, as can be depicted by the localization of the HOMO and LUMO orbitals as well as by the charge distribution between the ground and the excited state. The bond connecting the heterocyclic system of the molecule with the phenyl ring is also of significant importance because despite the fact that imposes the only degree of rotational freedom to the molecule, has been found to possess partial double bond character. The properties of the molecule were studied employing both semi-empirical and ab initio calculations whereas its fine electronic structure was explored using Bader's AIM theory.

Density Functional Theory Studies on Transimination of Vitamin B6 Analogues through Geminal Diamine Formation

A theoretical study on the transimination reaction in the gas phase of a molecular complex that consists of a Schiff base formed from a vitamin B6 model compound, methylamine, and one water molecule is reported. In this nonenzymatic environment, DFT calculations (B3LYP/6-31+G*) with full optimization of each intermediate and transistion state structure and a further study of the topology of the charge density function according to Bader's AIM theory are carried out. This work has allowed the detailed outline of the energy profile of the reaction leading to the geminal diamine formation and the description of the geometries of all the structures involved. The reaction determining step is the addition of the incoming amine onto the Schiff base and the main intermediate of the overall reaction is a geminal diamine structure. The mechanism also points out the reactive role of one water molecule by allowing the proton transfer between distant sites of the molecular complex by means of the formation of a concerted transition state.

Re-examination of the Solvolysis of Acyl Chlorides. Rethinking the Role of Both Carbonyl and Chloride

This letter describes a computational investigation into the hydrolysis mechanism of carbonyl compounds. Hydrolysis has previously been thought to be a very well-understood process. The molecules formaldehyde (CH2O), formyl chloride (HCOCl), and phosgene (COCl2) were used to probe the initial steps of the hydrolysis mechanism. A combination of quantum mechanics calculations and application of Bader's AIM analysis was used to study the mechanism. The results show that the carbon−oxygen double bond is more akin to the polarized bond between phosphorus and oxygen rather than to a true double bond such as that found in ethylene. Further, the results show that the initial step of the reaction is formation of a strongly hydrogen-bonded complex as opposed to direct addition of a nucleophile to the carbonyl center. Finally, the results show that chlorine plays a substantial role in stabilizing the carbocationic center resulting from the initial hydrogen bond formation. These results strongly suggest the mechanism...

Charge density and experimental electrostatic potentials of two penicillin derivatives.

Two penicillin derivatives, the active penamecillin and the inactive penamecillin-1beta-sulfoxide, were used to study the relationship between their charge density and their activity. Single crystals of both compounds were measured at the synchrotron beamline F1 at the HASYLAB/DESY, at 100 K and up to resolutions of around 0.4 A. Experimental charge densities were obtained by using the Hansen-Coppens multipole formalism. The cleavage of the amide bond in the beta-lactam ring is of paramount importance in the mechanism of action of penicillins. Topological analysis of this bond in terms of Bader's AIM theory showed that its strength is equal in both compounds; therefore a direct influence of bond strength on the activity can be ruled out. However, the two derivatives differ significantly in their experimental electrostatic potentials. These differences are discussed and provide further insight into the chemistry and activity of penicillins.

DFT Studies on Schiff Base Formation of Vitamin B6Analogues

A comprehensive study of Schiff base formation of vitamin B6 analogues by using DFT calculations (B3LYP/6-31+G*) and a study of the topology of the density charge function of the optimized structures according to Bader's AIM theory are carried out. Vitamin B6 analogues for the gas-phase calculations include one auxiliary water molecule. These calculations result in the description of the geometries of all the intermediates and transition structures along the reaction pathway, which can be divided in three parts: carbinolamine formation, dehydration, and imine formation. The carbinolamine is the main intermediate, and dehydration is the limiting step of the reaction, in accordance with experimental evidence. The details of the mechanism of carbinolamine formation highlights the key role of the auxiliary water molecule of the molecular complex as a true reactive for allowing the nucleophilic attack of the incoming amine to the carbonyl group.

Gas‐Phase Reaction Pathways from SiH4 to Si2H6, Si2H4 and Si2H2: A Theoretical Study

AbstractFor Abstract see ChemInform Abstract in Full Text.

Gas-Phase Reaction Pathways from SiH4to Si2H6, Si2H4and Si2H2: A Theoretical Study

Initial gas-phase reactions for a system containing silane (SiH4) and hydrogen (H2) were investigated using ab initio calculations at the MP2/6-311++g** level. Twenty-four minimum and 19 transition states were located on the potential energy surface of the neutral species containing one or two silicon atoms. The bonding nature of each species was elucidated by topological analyses of electron density using Bader's AIM theory. The reaction pathways were classified into three parts: Part (I) shows elimination of the first H2 and formation of disilane (Si2H6). Part (II) shows elimination of the second H2 and formation of five disilene (Si2H4) isomers. Part (III) shows elimination of the third H2 and formation of four disilyne (Si2H2) isomers. More energy is required to obtain species with less hydrogen content, and such species are more likely to be stabilized by a hydrogen bridged bond (Si−H−Si). Calculated IR spectra, dipole moments, and rotational constants were provided for comparison with the experiments.

Structure and Charge Density of a C60-Fullerene Derivative Based on a High Resolution Synchrotron Diffraction Experiment at 100 K

The experimental charge density of a highly substituted fullerene derivative, the Th-symmetrical dodekakis(ethoxycarbonyl)-C60-fullerene cocrystallized with difluorobenzene, C102H60O24·2C6H4F2, was determined, on the basis of a high-resolution synchrotron/CCD data set of more than 350 000 reflections. A full topological analysis, using Bader's AIM theory, was performed. Experimental bond critical point (BCP) properties, obtained by three multipole models, were compared to each other and to those derived by theoretical methods from HF/6-31G** and from B3LYP/6-31G** calculations. ρ(rBCP) vs bond distance relationships were investigated for the different experimental and theoretical models. Based on linear fits obtained for experimental model densities, ρ(rBCP) values of further C−C bonds can be predicted. Due to substitution, this C60 derivative has six chemically different C−C bonds. A statistical analysis of the BCP properties for these bonds was carried out to explore the reproducibility of different top...

Atomic properties of N(2)O(4) based on its experimental charge density.

Nitrogen dioxide, being known to exist as a dimer N2O4 in the crystal with a very long N-N bond length of 1.76 A, was crystallized at low-temperature conditions on a diffractometer. High-resolution X-ray data (sin(theta/lambda) = 1.249 A-1) were recorded with a CCD area detector to allow the generation of an experimental charge density distribution. By making use of Bader's AIM theory, zero-flux surfaces were calculated, and we examined atomic volumes and atomic charges obtained from this experiment and various theoretical calculations. Four commonly used methods of computing atomic charges (Mulliken, AIM, NPA, and CHELP) were considered. The AIM charges are rather independent from the used basis set. Interestingly, the evaluated atomic volumes are very similar between experiment and theory, although in theory isolated molecules are considered. For the long N-N bond a bond order n of approximately 0.5 was derived from a comparison with appropriate model compounds.

Comparison of different atomic charge schemes for predicting pKavariations in substituted anilines and phenols*

AbstractA number of different methods have been proposed for assigning partial charges to the atoms of a molecule, including both quantum chemical and empirical schemes. A reasonable expectation for any successful calculational scheme is that the atomic charges it produces should vary in a manner consistent with chemical intuition and, more specifically, that these variations should be correlated in a sensible way with experimental observations. Seven of the most popular atomic charge schemes (Bader's AIM chargesQAIM, electrostatic potential chargesQESP, GAPT chargesQGAPT, Gasteiger π chargesQGast, Löwdin chargesQLöw, Mulliken chargesQMul, and charges derived from natural population analysisQNPA) were tested for their ability to represent variations in the pKa's of 19 monosubstituted anilines and 19 monosubstituted phenols. In most cases the calculations were performed at the B3LYP/6‐311G** level of theory. For the substituted anilines, the amino nitrogen, anilinium proton, and total amino group charges were taken as representative regression parameters, and for the phenols, the phenolic hydrogen, phenoxide oxygen, and hydroxyl group charges were employed. Overall,QAIM,QLöw, andQNPAyielded the most successful correlations with the pKa's of these compounds, although for the phenol series,QGAPTandQMulalso yielded good results. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002

Novel point charge models: reliable instruments for­molecular electrostatic

AbstractA novel method to compute atomic charge distribution is proposed. The starting data for the computation are the topology of a molecule and electronegativities of either constituent atoms or atomic orbitals. The topology of a molecule is represented by a molecular graph or, in a more advanced model, by an orbital graph that reflects an orbital constitution of atoms. The distinctive feature of the method is that the starting atomic (orbital) electronegativities equilibrate in the same fashion that electrical potentials do in the nodes of a closed electrical network. Thus, the well‐developed formalism of the theory of electrical circuits was applied for computation of partial atomic charges. In addition, the problem of parametrization of halogens was solved using a specially developed procedures. Comparison of the obtained charges with those produced by means of various computational schemes [Partial Equalization of Orbital Electronegativities (PEOE), Mulliken population analysis, natural population analysis, Bader's AIM, method of generalized atomic polar tensors (GAPT) and an electrostatic potential‐based method, CHELPG] and with some molecular spectral characteristics proves that both models, but especially the orbital graph charge model, provide fast, convenient and reliable methods to calculate theoretically justifiable atomic charges for a variety of chemical species. The developed charge models are well suited for application in many areas of molecular modeling and QSAR/QSPR studies. Copyright © 2001 John Wiley & Sons, Ltd.