Aqueous solvent effects on the conformational space of tryptamine. Structural and electronic analysis.

The TRA (3-[2-aminoethyl]indole) is an important neurotransmitter with a close structural and chemical similarity to the neurotransmitter serotonin (5-hydroxytryptamine), and to melatonin (5-methoxy-N-acetyltryptamine), which plays a key role in daily human behavior. Moreover, TRA, and other indolic compounds are very efficient antioxidants. In this work the conformational space of TRA was scanned in aqueous solution, simulating the solvent by the polarizable continuum model. Geometry optimizations were performed at B3LYP/6-31+G** level. Electronic distributions were analyzed at a better calculation level, thus improving the basis set (6-311++G**). A topological study based on Bader's theory (atoms in molecules) and natural bond orbital (NBO) framework was performed. Structural changes found in solution were related with charge delocalization mechanisms, which explained the changes in the conformational relative population in aqueous phase. Solvent effects on molecular electrostatic potential (MEPs) were also quantified and rationalized through charge delocalization mechanisms, thus connecting changes in MEPs with changes in structure, bond polarization, orbital bonding populations, natural charges, and bond topological properties. Moreover, polarizabilities and dipolar moments were calculated. All conformers were taken into account. Our results are the first prediction of TRA polarizabilities. The results reported contribute to the understanding of the structure, stability and reactivity of TRA and other indole derivatives.

Topological properties of some PhSeX compounds.

A theoretical study on the series of compounds "PhSeX", where Ph = phenyl, Se = selenium and X = Cl, Br, I, CN or SCN, is reported and compared with previously reported experimental data. The molecular geometry for these PhSeX compounds was studied at the DFT/B3LYP level of calculation by means of the 6-311G(d,p) basis set. The equilibrium structures of the molecules were dependent on the method employed to compare the known solid structures. A topological study of the calculated PhSeX species, based on the AIM theory, was carried out to gain a deeper insight into the bonding nature and to find an explanation for the structural diversity exhibited by these PhSeX compounds. The results reported herein illustrate the subtle differences in the solid-state structures of PhSeX compounds.

Structural and electronic properties of Z isomers of (4α→6´´,2α→O→1´´)-phenylflavans substituted with R = H, OH and OCH3 calculated in aqueous solution with PCM solvation model.

In the search for new antioxidants, flavan structures called our attention, as substructures of many important natural compounds, including catechins (flavan-3-ols), simple and dimeric proanthocyanidins, and condensed tannins. In this work the conformational space of the Z-isomers of (4α→6´´, 2α→O→1´´)-phenylflavans substituted with R = H, OH and OCH(3) was scanned in aqueous solution, simulating the solvent by the polarizable continuum model (PCM). Geometry optimizations were performed at B3LYP/6-31 G level. Electronic distributions were analyzed at a better calculation level, thus improving the basis set (6-311++G). A topological study based on Bader´s theory (atoms in molecules) and natural bond orbital (NBO) framework was performed. Furthermore, molecular electrostatic potential maps (MEPs) were obtained and thoroughly analyzed. The stereochemistry was discussed, and the effect of the solvent was addressed. Moreover, intrinsic properties were identified, focusing on factors that may be related to their antioxidant properties. Hyperconjugative and inductive effects were described. The coordinated NBO/AIM analysis allowed us to rationalize the changes of MEPs in a polar solvent. To investigate the molecular and structural properties of these compounds in biological media, the polarizabilities and dipolar moments were predicted which were further used to enlighten stability and reactivity properties. All conformers were taken into account. Relevant stereoelectronic aspects were described for understanding the stabilization and antioxidant function of these structures.

QSPR Study of Valproic Acid and Its Functionalized Derivatives.

This work establishes a Quantitative Structure-Property Relationships (QSPR) based analysis with the aim of interpreting both the structural and electronic properties of the polar region of valproic acid and its derivatives, in terms of stabilizing intramolecular interactions related to the involved substituents. We consider ten different calculated properties as dependent variables for the QSPR models: the bond lengths C8 O9 , C8 X10 , and the percentage of s-character of the natural hybrids forming the bonding σ orbitals of the O9 C8 X10 region. The representative descriptors are the charges transferred during donor/acceptor interactions around this function calculated at the B3LYP/6-311++G**(6d,10f) level of theory, and/or hybrid descriptors derived therefrom. The models so established result simple, predictive, and have a quite direct physical meaning.

Conformational and stereoelectronic investigation of tryptamine. An AIM/NBO study.

UNLABELLED: Due to the free radical scavenger properties of Tryptamine (TRA), as well as of others indole derivatives, it is in our interest to explore deeply the stereoelectronic aspects that would be relevant in their stabilization and antioxidant activity. In this work the conformational space of TRA was scanned using molecular dynamics complemented with functional density calculations at B3LYP/6-31 + G** level. Twenty one conformers of lowest energy were obtained, their electronic distributions were analyzed at a higher calculation level, thus improving the basis set (B3LYP/6-311++G**). A topological study based on Bader's theory ( AIM: atoms in molecules) and natural bond orbital (NBO) framework was performed. The study was enriched by a deep analysis of maps of molecular electrostatic potential (MEP) through a coordinated NBO/AIM analysis. The conformational preferences were explained by hyperconjugative interactions, which were revealed by NBO data. Because radical scavenging by indolic compounds is strongly modulated by their functional residues our study was related to similar analysis done previously on Indole and 1H-indole-3-acetic acid (IAA). Therefore, the conformational space of TRA was studied from a new perspective focusing on a deep analysis of the geometric and electronic properties of TRA conformers. The changes of the electronic distribution introduced by the substituent and the conformational flexibility of the side chain were addressed. The results reported contribute to the understanding of the structure, stability and reactivity of TRA and others indole derivatives.

Study of the structural and electronic properties of valproic acid and new derivatives used as anticonvulsant agents.

The conformational and electronic characteristics of the polar O(9)═C(8)-X(10) moiety in the anticonvulsant valproic acid (Vpa) drug and some of their amides and ester derivatives are analyzed at the B3LYP level using the 6-31+G(d,p) and 6-311++G(d,p) 6d,10f basis sets. Exploring the delocalization of the electron density of the O(9)═C(8)-X(10) moiety by means of ELF, NBO, and AIM calculations, we found that the bending away from coplanarity of the atoms in O(9)═C(8)-X(10) is accompanied by a three-dimensional arrangement of donor and acceptor proton units closing nearly planar pseudorings of four, five, and six members arising from stabilizing interactions around the O(9)═C(8)-X(10) backbone. From the structure-property relationship analysis, we explain the origin of the change in the structural parameters and atomic charges in the polar moiety.

Electronic structure and conformational properties of 1H-indole-3-acetic acid.

UNLABELLED: The conformational space of 1H-Indole-3-Acetic Acid (IAA) was scanned using molecular dynamics at semiempirical level, and complemented with functional density calculations at B3LYP/6-31G** level, 14 conformers of lowest energy were obtained. Electronic distributions were analyzed at a higher calculation level, thus improving the basis set (B3LYP/6-311++G**). A topological study based on Bader's theory ( AIM: atoms in molecules) and natural bond orbital (NBO) framework performed with the aim to analyze the stability and reactivity of the conformers allowed the understanding of electronic aspects relevant in the study of the antioxidant properties of IAA. Intramolecular hydrogen bonds were found and were characterized as blue-shifting hydrogen bonding interactions. Furthermore, molecular electrostatic potential maps (MEPs) were obtained and analyzed in the light of AIM and NBO results, thus showing subtle but essential features related not only to reactivity but also with intramolecular weak interactions, charge delocalization and structure stabilization.

Theoretical studies and vibrational spectra of 1H-indole-3-acetic acid. Exploratory conformational analysis of dimeric species.

Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A exploratory study of the conformational space of dimeric species was performed. Our analysis showed that dimeric forms predicted theoretically contribute distinctively to the assignments of experimental results. These structures are defined by the orientation of the acetyl moieties with respect to the plane of indole ring. The dimers are formed by two symmetrical IAA monomers (one of them with the acetyl moiety upward oriented, Re-face, and the other isomer having the acetyl moiety downward oriented, Si-face) in tail-to-tail way. The X-ray geometry and FTIR vibrational frequencies were compared with the results of DFT calculations. A conformational equilibrium involving the non-equivalent IAA dimers: CCT-CCT, A(+)A(+)T-A(-)A(-)T, A(+)A(-)T-A(-)A(+)T, and A(+)CT-A(-)CT was found. The relation of the conformational properties of the IAA molecule with the features of the vibrational spectra was described in detail. The band assignments were discussed as related to the conformations properties. Our analysis shows the significance of the theoretical study of the conformational space of the monomeric molecule in the rationalization of experimental results.

Theoretical study of Z isomers of A-type dimeric proanthocyanidins substituted with R=H, OH and OCH3: stability and reactivity properties.

The stereochemistry of A-type dimeric proanthocyanidins was studied, focusing on the factors that determine it, and the changes that occur with R = OCH3, R' = H, and R = OH, R' = H as substituents, starting with the study of the conformational space of each species. Using molecular dynamics at a semiempirical level, and complementing with functional density calculations, two conformers of lowest energy were characterized for R = H, eight conformers for R = OH, and three conformers for R = OCH3. Electronic distributions were analyzed at a higher calculation level, thus improving the basis set. Intramolecular interactions were examined and characterized by the theory of atoms in molecules (AIM). Detailed natural bond orbitals (NBO) analysis allowed the description of subtle stereoelectronic aspects of fundamental importance for understanding the stabilization and antioxidant function of these structures. The study was enriched by a deep analysis of maps of molecular electrostatic potential (MEP). The coordinated analysis of MEP, together with the NBO and AIM results, allowed us to rationalize novel distribution aspects of the potential created in the space around a molecule.

Theoretical characterization of SOME amides and esters DERIVATIVES of valproic acid.

The equilibrium structures, the planarity of the C(=O)X linkage and the nature of the chemical bond in the Y-C(=O)-XR(1)R(2) [where: Y= -CH-(CH(2)-CH(2)-CH(3))(2), X=N,O and R(1), R(2)= H; alkyl and aryl groups and lone pair electrons (lp)] molecular fragment of derivates of Valproic acid (Vpa) with antiepileptic activity were studied systematically by means of B3LYP calculations and topological analysis of the electron localization function (ELF). The covariance parameter cov[Omega(i), Omega(j)] reveals a dominating delocalization effect between the lone pair V(O(1)), V(X) and the electron density of the H-C and H-X(1) bonds resulting from the existence of not only non-conventional intramolecular hydrogen bonding patterns as C-H...O/N but also a weak closed-shell stabilizing interaction type arising from a dihydrogen bonding as C-H...H-N, where H...H contacts at a significantly shorter distance than twice the hydrogen atom van der Waals radius. The analyzed data derived from ELF domains were found to be in agreement with the known features and properties of the hydrogen bonding interactions discussed in this work.

Conformational and electronic (AIM/NBO) study of unsubstituted A-type dimeric proanthocyanidin.

UNLABELLED: The conformational space of the unsubstituted A-type dimeric proanthocyanidin was scanned using molecular dynamics at a semiempirical level, and complemented with functional density calculations. The lowest energy conformers were obtained. Electronic distributions were analysed at a higher calculation level, thus improving the basis set. A topological study based on Bader's theory ( AIM: atoms in molecules) and natural bond orbital (NBO) framework was performed. Furthermore, molecular electrostatic potential maps (MEPs) were obtained and analysed. NMR chemical shifts were calculated at ab initio level and further compared with previous experimental values; coupling constants were also calculated. The stereochemistry of the molecule is thoroughly discussed, revealing the key role that hyperconjugative interactions play in defining experimental trends. These results show the versatility of geminal spin-spin coupling (2)J(C-1',O) as a probe for stereochemical studies of proanthocyanidins.

Spectroscopic and theoretical study of 2-acetylphenyl-2-naphthoate.

Mid-, far-infrared and Raman vibrational spectra of 2-acetylphenyl-2-naphthoate have been measured at room and low temperatures. The molecule was also analyzed by means of ab initio calculations. The conformational space has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest energy conformers 2-acetylphenyl-2-naphthoate as obtained in the simulations. The vibrational frequencies and the (1)H and (13)C NMR chemical shifts were assigned using functional density calculations. The theoretical chemical shift values were compared with the experimental ones. The molecular electrostatic potential maps were obtained and analyzed.

Topological insights into the nature of the halogen-carbon bonds in dimethylhalonium ylides and their cations.

In this study the nature of the bonding in a series of dimethylhalonium ylides (fluoronium, chloronium, bromonium and iodonium) was analyzed by means of topological methodologies (AIM and ELF analysis), to document the changes in the nature of the C-X bonds (X = F, Cl, Br, I) upon the series. For the sake of comparison the same study was performed on the corresponding dimethylhalonium cations (XC 2H 6 (+)) and the XCH 3 series. The wave functions used for the topological analysis were obtained at B3LYP level using extended triple-zeta basis sets. The formation of the cationic XC 2H 6 (+) structures can be interpreted to arise from the interaction between the XCH 3 and CH 3 (+) moieties. The resultant structures can be explained in terms of the superposition of two electrostatically interacting and two dative mesomeric structures. The halogen-carbon bonds have all the characteristics of the charge-shift (CS) bonds. The analysis of the C-X bond in the XC 2H 5 series shows a progressive reinforcing of the CH 3X-CH 2 bond, from FC 2H 5 that can be considered as formed from two fragments, FCH 3 and CH 2, to IC 2H 5, in which the CH 3I-CH 2 bond has all the features of a multiple bond involving atoms bearing lone pairs. Particularly interesting is BrC 2H 5, in which a special type of bond (hybrid covalent-dative double bond) has been characterized. The energetic stability of the XC 2H 5 structures with respect to the dissociation into the XCH 2 + CH 3 and XCH 3 + CH 2 ground-state fragments was studied in detail.

Vibrational spectra, NMR and theoretical studies of the enantiomers and rotamers of alpha-cypermethrin.

NMR, infrared and Raman vibrational spectra of alpha-cypermethrin have been measured at room temperature. Infrared spectra were also recorded to low temperature. The spectra were analyzed by means of ab initio calculations. The conformational space of both enantiomers and some rotamers A, B and C of alpha-cypermethrin has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest-energy conformers of each species as obtained in the simulations. The vibrational frequencies and the 1H and 13C NMR chemical shifts were assigned using functional density calculations. The molecular electrostatic potential maps were obtained and analyzed.

Three-center-two-electron and four-center-four-electron bonds. A study by electron charge density over the structure of methonium cations.

We study the electronic density charge topology of CH(5)(+) species 1 (C(s)()), 2 (C(s)()), and 3 (C(2)(v)) at ab initio level using the theory of atoms in molecules developed by Bader. Despite the reports of previous studies concerning carbocationic species, the methane molecule is protonated at the carbon atom, which clearly shows its pentacoordination. In addition to the fact that hydrogen atoms in the methonium molecule behave in a very fluxional fashion and that the energy difference among the species 1, 2, and 3 are very low, is important to point out that two different topological situations can be defined on the basis of our study of the topology of the electronic charge density. Then, the species 1 and 2 present a three-center-two-electron (3c-2e) bond of singular characteristics as compared with other carbocationic species, but in the species 3, the absence of a 3c-2e bond is noteworthy. This structure can be characterized through the three bond critical points found, corresponding to saddle points on the path bonds between the C-H(2,3,5) that lie in the same plane. These nuclei define a four-center interaction where the electronic delocalization produced among the sigma(C-H) bonds provide a stabilization of the three C-H bonds involved in this interaction (the remaining two C-H bonds are similar to those belonging to the nonprotonated species). Our results show that bonding situations with a higher number of atom arrays are possible in protonated hydrocarbons.

Study of the Topological Properties of Some Pseudohalides.

The pseudohalide principle has been used extensively in nonmetal chemistry to predict the structure and stability of many molecular species. The 1,2,3,4-thiatriazole-5-thiolate anion, CS2N3(-), is of particular interest. In a short communication we have recently reported the topological study of some CS2N3(-)containing species reported by Crawford et al. Previous reports on these compounds showed that in covalent derivatives not only does the ring remain intact but also the site of attachment of the R group is most likely at the exocyclic sulfur atom in contrast to the previously suggested N-R connectivity. Therefore, the structure and bonding of derivatives of the CS2N3(-) moiety is clearly an important question. With that in our mind, we undertook a topological analysis, based on the AIM theory, to gain more insight into the bonding in covalent derivatives of the CS2N3(-) moiety, trying to find an explanation to the origin of the N-H and S-H connectivities. The question is which is the reason that makes all the covalent derivatives prefer the S-R connectivity while the hydracid has an N-H one.

Some electronic correlation effects in the topological analysis of the Laplacian of the electronic charge density in C-n-butonium cations.

In this work, we present a topological study of the Laplacian of the electronic density using a 6-311++G basis set, at Hartree-Fock (HF) and second-order Møller-Plesset (MP2) (full-electron and frozen-core) levels of theory, for the carbocations 2-C-n-butonium generated upon the insertion of a proton into the secondary C-C bond during the protonation of n-butane. The charge concentration, CC, critical points of the Laplacian distribution at each valence shell, VS, of carbon atoms, and the charge concentration closer to hydrogen atoms are studied. Also, the bonding critical points of the electronic density are analyzed. We analyze some effects that Coulomb correlation has on topological features of the electronic distribution. It is shown that they are mainly reflected in a decreasing of the charge concentrations at the VS and in a contraction of the VS to the nuclei. They are more pronounced over C-C bonds than in C-H bonds. The sensitivity of some parameters derived from this topological analysis to the correlation effect of core electrons and subtle effects related to hyperconjugative interactions are shown. Some consequences of different schemes (double and triple split-valence basis set with diffuse and polarization functions) in the definition of subtle VS charge concentrations at 3c-2e bond paths are presented. It is also demonstrated here how the facts that allow us to understand the MP2 stability order found in the carbocationic species 2-C-n-butonium > 1-C-n-butonium > 2-H-n-butonium > 1-H-n-butonium are similarly depicted at correlated and uncorrelated levels of calculation.