On the rhodanines and their presence in biologically active ligands

An innovative use of cluster analysis is presented to compare the output from different levels of theory. A dendrogram shows the relative energies of the tautomers of methylidene rhodanine (5-methylene-2-thioxo-thiazolidin-4-one), computed by the semiempirical molecular orbital method AM1, are remarkably similar to the ab initio values from the LANL2DZ++(d,p) basis set, which involves effective core potentials augmented by polarization and diffuse functions. However, the optimized bond lengths and bond angles at the AM1 and AM1/SM1 levels do not agree well with those obtained at the 6–31G^* and LANL2DZ++(d,p) levels of theory or with experiment. Database searching is used to obtain an indication of how common the rhodanine ring is. The prevalence of rhodanine-containing compounds of pharmaceutical interest is very small despite the fact that the compounds exhibit a wide variety of bioactivity.     

Reaction of arylpyrotartaric acids with rhodanine

The reaction of arylpyrotartaric acids with rhodanine in ethanol in the presence of aqueous ammonia and ammonium chloride has yielded 5-(-aryl--carboxyethylidene)rhodanines.     

Spectroscopic investigations and ab initio computations of the dye Chromotrope 2R

Detailed analysis of the NIR FT-Raman, FT-IR and UV–visible spectra of the dye Chromotrope 2R (C2R) has been performed. The optimized geometry of the dye is theoretically computed with the HF and DFT levels using the standard 6-31G(d) and LANL2DZ basis sets. Optimized geometry and vibrational spectra indicate that the major species in the solid state are the trans form of hydrogen bonded hydrazone tautomer. The effect of H-bonding in stabilizing a particular type of structure is also discussed. The most preferred trans-configuration for its photochemical activity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. The optimized geometries and calculated vibrational wavenumbers are evaluated via comparison with experimental values. Electronic spectra are in accordance with the nature of the electronic transitions predicted by time-dependent B3LYP/DZ calculations.     

Theoretical study of [Li(H2O)n]+ and [K(H2O)n]+ (n = 1−4) complexes

The geometries, successive binding energies, vibrational frequencies, and infrared intensities are calculated for the [Li(H₂O)_n]⁺ and [K(H₂O)_n]⁺ (n = 1?4) complexes. The basis sets used are 6-31G* and LANL 1DZ (Los Alamos ECP +DZ ) at the SCF and MP 2 levels. There is an agreement for calculated structures and frequencies between the MP 2/6-31G* and MP 2/LANL 1DZ basis sets, which indicates that the latter can be used for calculations of water complexes with heavier ions. Our results are in a reasonable agreement with available experimental data and facilitate experimental study of these complexes. © 1995 John Wiley & Sons, Inc.     

Association of Diphenylguanidine and Quantum-Chemical Calculations of the Structure of Its Cyclic Dimers

The frequencies and intensities of the two tautomeric structures of the N, -diphenylguanidine monomer and its hydrogen-bonded cyclic dimers were calculated for structure elucidation of the monomer and dimer forms of this compound and identification of the stretching vibration band NH of this molecule in solution. Ab initio HF/3-21G and B3LYP/6-31G(d,p) calculations of DPG monomers and cyclic associates suggest that the asymmetric tautomer is dominant, proving that the dimer structures with two C=(Ph)N...H–NPh hydrogen bonds prevail in solution. An assignment of IR absorption frequencies of DPG in solution is suggested.     

Synthesis, antihistaminic action and theoretical studies of (4-methoxybenzyl)(1,4,5,6-tetrahydropirimidin-2-yl)amine hydroiodide

In this study, (4-methoxybenzyl)(1,4,5,6-tetrahydropyrimidin-2-yl)amine hydroiodide (2) was synthesized by reaction of 2-methylmercapto-1,4,5,6-tetrahydropyrimidine hydroiodide (1) and 4-methoxybenzylamine. The synthesized compound was tested for its in vitro H1-antihistaminic activity on guinea pig trachea. A promising bronchorelaxant effect of 2 was observed in histamine-contracted guinea pig tracheal chain via H1 receptor antagonism. In addition, the molecular geometry and gauge including atomic orbital (GIAO) ¹H chemical shift values of the title compound in the ground state were calculated using the density functional method (DFT/UB3LYP) and Hartree–Fock (HF) approach using 6–311G+(d), 6–311G+(d,p), LANL2DZ, DGDZVP, and DGDZVP2 basis sets and compared with the experimental data. According to the experimental and theoretical results, HF/6–311G+(d) showed a better fit to experimental values in evaluating ¹H-nuclear magnetic resonance (NMR) chemical shift values. Theoretical studies supported our findings, revealing the N₁₂ atom as the most nucleophilic. In addition, other structures of the compound such as the aromatic ring and OCH₃ group increased this property.     

Theoretical insight into structural and electronic properties of cationic Scn+ (n=2-13): A benchmark study

Geometric, thermodynamic and electronic properties of cationic scandium clusters are studied. Geometric optimizations and stable spin states of Sc₂⁺ are assessed on high level ab-initio coupled cluster method CCSD(T) with different dunning correlation consistent basis sets (aug-cc-pVDZ, aug-cc-pVTZ and aug-cc-pVQZ). Then, 23 DFT functionals belonging to different classes are evaluated at 6-31G (d), LANL2MB, LANL2DZ and Def2-SVP basis sets, and the results are compared with the benchmarked coupled cluster calculations. Due to excellent correlation, PBEPBE/LANL2DZ was chosen to perform calculation of higher scandium cationic clusters Sc_n⁺ (n = 3-13). In addition, we explored relative stability, binding energies, second order energy differences, vertical ionization energies, vertical electron affinities and HOMO-LUMO gaps. Moreover, these results are also compared with the neutral scandium clusters.     

Intramolecular Hypervalent X←X Interaction in Mono- and Bicyclic Heteroelement Compounds Containing Se and Te Atoms

Chalcogen-containing heterapentalene and quasimonocyclic compounds having SeÄSeÄSe and TeÄTeÄTe triads or SeÄSe and TeÄTe diads were studied by the ab initio [MP2(full)/6-31G**, MP2(fc)/6-31+G**, and MP2(fc)/LANL2DZ] and DFT methods (B3LYP/6-31G^**, B3LYP/6-31+G^**, and B3LYP/LANL2DZ). Heterapentalene compounds were found to be stable as planar bicyclic structures having a C _2v symmetry. The stability of quasimonocycic -chalcogenovinyl aldehydes increases with increase in the electron-acceptor power of the substituent at the X atom.     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Benzoid–Quinoid tautomerism of schiff bases and their structural analogs: LVII. 2-[(3-oxo-5-phenylpyrazolidin-1-yl)methylidene]-1<Emphasis Type="Italic">H</Emphasis>-indene-1,3(2<Emphasis Type="Italic">H</Emphasis>)-dione

Potentially tautomeric azomethine imide, 2-[(3-oxo-5-phenylpyrazolidin-1-yl)methylidene]-1H-indene- 1,3(2H)-dione, has been synthesized by condensation of 5-phenylpyrazolidin-3-one with 2-(hydroxymethylidene)-1H-indene-1,3(2H)-dione. According to the IR, ¹H and ¹³C NMR, and electronic absorption spectroscopy data and DFT B3LYP/6-311++G(d,p) quantum chemical calculations, the title compound in solution exists as planar tricarbonyl tautomer stabilized by intramolecular hydrogen bond between the NH proton of the pyrazolidine fragment and carbonyl oxygen atom of the indene fragment. Its crystal structure was determined by X-ray analysis.     

Tautomerism of rhodanine

Semiempirical (MINDO/3, AM1, PM3, MNDO) and ab initio (4-31G and 4-3IG + dAO/S basis sets) calculations on the relative stabilities and structures of the five potential tautomeric forms of rhodanine are reported. It is shown that all methods (excepting PM3) predict as most stable 2-thioxo-4-thiazolidinone. These results correspond to the known experimental data. The infrared spectrum of rhodanine was recorded for the region 4000-150 cm^–1, and the characteristic bands were compared with AM1 and 4-31G + dAO/S calculated frequencies. The transition states between five pairs of all possible tautomeric forms of the rhodanine were found by the AM1 method.     

Crystal structure and rotational barrier of octakis(bromomethyl)naphthalene

Octakis(bromomethyl)naphthalene (4) adopts in the crystal a chiral conformation with a helical central naphthalene core and the bromomethyl groups disposed in an alternate up-down "in" arrangement. According to MM3 calculations, this conformation is less stable than the corresponding all alternated "out" form, while B3LYP/LANL2DZ calculations suggest the opposite stability order. The topomerization barrier (16.0 kcal mol(-1)) is ascribed to an enantiomerization process requiring 180 degrees rotation of all the bromomethyl groups and reversal of the helical sense of the naphthalene core.     

Theoretical studies of organometallic compounds. III. Structures and bond energies of FeCHn and FeCH (n = 1, 2, 3)

The geometries and dissociation energies for the Fe? C and C? H bonds of FeCH_n and FeCH (n = 1, 2, 3) have been calculated by ab initio quantum mechanical methods using different effective core potential models and Møller–Plesset perturbation theory. The HW3 ECP model, which has a configuration [core] (n?1)s², (n?1)p⁶, (n?1)d¹, (n)s^m for the transition metals, is clearly superior to the larger core LANL1DZ ECP model with the configuration [core] (n?1)d¹, (n)s^m. The Fe? C bond energies calculated at correlated levels using the HW3 ECP are in much better agreement with experiment than the LANL1DZ results. This effect is mainly due to the higher number of correlated electrons rather than the inclusion of the outermost core electrons in the Hartree–Fock calculation. At the PMP4/HW3TZ/6-31G(d)//MP2/HW3TZ/6-31G(d) level, the theoretically predicted Fe? C bond energies for FeCH are in the range of 80% of the experimental values and have nearly the same accuracy as all-electron calculations using large valence basis sets and the MCPF method for the correlation energy. © 1992 by John Wiley & Sons, Inc.     

Small Ligated Organometallic $${{\hbox {Pd}}}_{n}$$ Clusters ($$n= 4{-}12$$n=4-12): A DFT Investigation

DFT calculations were carried out at the BP86/LANL2DZ level of theory to probe the structures and relative stabilities of small and medium size ligated palladium clusters. Results show that optimized geometries satisfactorily mimic experimental structural data. Observed cluster electron counts generally deviate from the expected Wade–Mingos electron counts because of the presence of several non-conical T-shaped \({\hbox {ML}}_{3}\) fragments in the clusters. These species are thermodynamically stable with substantial HOMO–LUMO gaps.     

Hydrogen bonding: A molecular orbital treatment by the EHT and the CNDO/2 methods of methanol and of formic acid

By both the EHT and the CNDO/2 calculations, the linear dimer of methanol is found to be more stable than the cyclic dimer. The hydrogen bonds in the trimer are stronger than those in linear dimers. The proton potential function, charge densities, and overlap populations in the linear dimer of methanol have been obtained. The CNDO/2 calculations show that the cis-form of formic acid is more stable than the trans-form, in agreement with experimental data. The cyclic dimer of formic acid is more stable than the open dimer. The -form of formic acid trimer is more stable than the -form. The proton potential function and the charge densities in the cyclic dimer of formic acid have been obtained. The CNDO/2 method gives more realistic proton potential functions for the dimers of methanol and formic acid. The O ... O stretching force constant in the dimers of methanol and formic acid have been estimated to be 0.13 × 10⁵ dynes/cm and 0.27 × 10⁵ dynes/cm, respectively, in agreement with experimental data.     

Hydrogen bonding in potassium hydrogen carbonate studied by compton scattering on single crystals

Compton spectra excited by ²⁴¹Am radiation have been measured on thin single-crystal slices with the scattering vector oriented parallel and perpendicular to the pair of hydrogen bonds in the (HCO₃) dimers as well as to the plane of the dimers. the reciprocal form factors extracted from the spectra are strongly anisotropic with two extra zero passages in the direction of the hydrogen bonds. the results are in very satisfactory agreement with theoretical data that are calculated for the dimer with and without additional point charges simulating the neighboring ions in the crystal. The calculations have been done with Gaussian basis sets of double-zeta quality within the Hartree–Fock approximation. The theoretical reciprocal form factors of the monomer HCO and the dimer show only small differences in the directions perpendicular to the hydrogen bonds, whereas the differences in the hydrogen bond direction are remarkable and account for the experimentally observed features. In comparison to this effect the influence of the neighboring ions by their charges is much smaller, which is even true when taking into account the influence of the neighboring dimers in the crystalline stack in more detail by symmetrical orthogonalization of the combined wave functions. The same orthogonalization procedure applied to a pair of monomers in the spatial arrangement of the dimer yields a reciprocal form factor that in the experimentally reliable range above 1.8 Å accounts for most of the dimerization effect in the direction of the hydrogen bonds. Thus also for this prototype of paired hydrogen bonds (cf., carboxylic acids, DNA, and RNA), it confirms our earlier experimental finding on liquid water now unambiguously, namely that, in the same way as the cohesion in ionic crystals, hydrogen bond formation in bulk matter is distinctly dominated by electrostatic attraction, which is compensated by repulsion owing to the Pauli principle.     

Theoretical and Experimental Studies on the Metal Complex of Diethylenetriamino-trioxo-molybdenum(VI) [MoO_3(NH_2C_2H_4NHC_2H_4NH_2)]

1 INTRODUCTION Molybdenum is a biologically important trace ele- ment that occurs in the redox-active sites of moly- bdoenzymes involving in nitrogen, sulfur or carbon metabolism. The structural chemistry of molybde- num complexes has aroused considerable interest in view of its higher oxidation states to form a number of compounds containing MoO groups, and informa- tion on these is very useful in understanding the behavior of MO groups generally[1~3]. Molybdenum oxide-based solids hav…     

LANL2DZ basis sets recontracted in the framework of density functional theory

In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.