Semi-empirical Quantum Mechanical Calculations Research Articles

Transesterification of substituted ethanols - modelling studies

Kinetic and molecular modeling of transesterification of ethyl acetate and substituted ethanols with porcine pancreatic lipase (PPL) and Candida cylindracea lipase (YL) is studied. Competitive product inhibition model is able to explain the observed behaviour well. The molecular dimensions of the substrates and the products, thermodynamic parameters and charges were estimated by molecular modelling based on minimum energy conformation and semi empirical quantum mechanical calculations. A strong correlation exists in the case of YL between conversion and (a) the cross sectional area of the alcohols, (b) difference between minimum energies of ester and alcohol, and (c) difference between the electrostatic potential volume of ester and alcohol. Only a weak correlation exists between these parameters, in the case of PPL whereas a strong correlation exists for PPL between conversion and charge on the alcohol oxygen of the substrate. Linear regression equations were developed for predicting the conversion based on these factors. Artificial neural networks (ANN) were employed to bring out the dependence of the catalytic activity on the molecular structure of the substituted ethanol. ANN model with charge on oxygen and molecular weight seems to fit the maximum reaction velocity in the case of PPL very closely. In the case of YL, ANN model with electrostatic potential volume difference and van der Waals volume fits the data satisfactorily. The variation of the maximum velocity with these parameters was also predicted using artificial neural network analysis. These studies indicate that both the lipases behave in different manner for the transesterification reaction.

Spectral characteristics of various prototropic species of 2-(3′-aminophenyl)pyrido[3,4-d]imidazole

Spectral characteristics of the prototropic species of 2-(3′-aminophenyl)pyrido [3,4-d]imidazole (3-APPI) have been studied in three non-aqueous and aqueous solvents, using absorption, fluorescence excitation and fluorescence spectroscopy, as well as, time dependent spectrofluorimetry. Acid concentration in ether is controlled by trifluoroacetic acid (TFA), whereas in other three solvents H 2SO 4 is used. Semi-empirical quantum mechanical calculations (AM1) and density functional theory (DFT) calculations have been carried out on all kinds of neutral and ionic species. Combining the experimental and theoretical results, the spectral characteristics have been assigned to various cationic and monoanionic species. It has been shown that: (i) only one kind of monoanion (MA) is formed by the deprotonation of N H moiety and one kind of trication (TC), (ii) two kinds of monocations (MC1 and MC3) in the ground (S 0) and first excited singlet (S 1) states in polar aprotic and protic solvents, whereas only one monocation (MC3) is formed in ether + TFA system. p K a values for the various prototropic reactions were determined in S 0 and S 1 states and discussed.

Spectral characteristics of 2-(2′-hydroxy-3′-pyridyl)benzimidazole: effects of solvents and acid or base concentrations

Absorption, fluorescence and fluorescence excitation spectroscopy and time dependent fluorimetry have been used to study the spectral characteristics of 2-(2′-hydroxy-3′-pyridyl)benzimidazole (2-H3PyBI) in different solvents and at different acid–base concentrations. Observation of only one small Stokes shifted fluorescence band reveals the absence of excited state intramolecular proton transfer (ESIPT). 2-H3PyBI is mainly present as the keto form even in cyclohexane. First site of protonation is imidazole nitrogen atom in both ground (S 0) and first excited singlet state (S 1). Dication in S 0 state is formed by protonating exo carbonyl group and pyridine nitrogen in S 1 state. Deprotonation occurs from >N–H moiety of pyridone, followed by structural reorganization to yield enolate ion. AM1 semi-empirical quantum mechanical and density functional theory (DFT) calculations have been used to assign the structure of neutral species and the site of protonation and deprotonation of 2-H3PyBI. Dissociation constants of various prototropic equilibria were determined and discussed. Theoretical calculations have been carried out to find the cause for the absence of ESIPT.

Synthesis, crystal structure and molecular conformation of (±)-1-oxoferruginol and (±)-shonanol

Abstract (±)-1-oxoferruginol and (±)-shonanol, two potential intermediates in the synthesis of tricyclic diterpenoid ferruginol, have been prepared and crystal structures of the compounds have been investigated using single-crystal X-ray diffraction data. The methyl groups of the isopropyl moiety in (±)-shonanol are disordered over two positions with occupation factors 0.65(1) and 0.35(1), respectively. Although the chemical structures of two compounds are very similar, a C—C single bond in the terminal six-membered ring of (±)-1-oxoferruginol is replaced by a C=C bond in (±)-shonanol, the quantitative isostructurality index calculations indicate that the structures are not isostructural. Intermolecular O—H…O hydrogen bonds between pairs of molecules in the compounds related by center of inversion lead to characteristic dimers forming R2 2(16) rings. The molecular conformation of (±)-1-oxoferruginol obtained from the semi-empirical quantum mechanical AM1 calculation shows good agreement with the X-ray structures.

Synthesis and structural characterization of some Schiff bases derived from 4-[{(aryl)imino}ethyl]-3-methyl-1-(4′-methylphenyl)-2-pyrazolin-5-one and spectroscopic studies of their Cu(II) complexes

Abstract A series of novel bidentate ligands have been synthesized by the condensation of 4-acetyl-2,4-dihydro-5-methyl-2-(4′-methylphenyl)-3H-pyrazol-3-one and various aromatic amines. All of these ligands have been characterized on the basis of elemental analysis, IR, 1H and 13C{1H} NMR data. The molecular geometries of five of these ligands have been determined by single crystal X-ray study. Crystallographic study reveals that these ligands exist in the amine-one tautomeric form in the solid state. NMR study also suggests the existence of the amine-one form in solution at room temperature. The reaction of these ligands with copper(II) resulted in the formation of mononuclear octahedral complexes of the general formulae [CuL2(H2O)2], with water molecules at the axial positions. These complexes were characterized on the basis of analytical and spectroscopic data. Thermal analyses of these complexes were also carried out. Magnetic moment measurements of these complexes at room temperature correspond to one unpaired electron. An ESR study of all these complexes in solution at room temperature, and also under frozen conditions at liquid nitrogen temperature, is consistent with the distorted octahedral geometry of the metal ion in these complexes. Semi-empirical quantum mechanical calculations (PM3) have been performed on the ligands to get charges over the coordinating atoms. A fairly good linear relation was found between the charges over the coordinating atoms of the ligands and the ligand field transition energies.

Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase (ubiA transferase) and characterization of potential active sites

4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligoprenyltransferase or any structurally related enzyme is known. Knowledge of the tertiary structure and possible active sites is, however, essential for understanding the catalysis mechanism and the substrate specificity. With homology modeling techniques, secondary structure prediction tools, molecular dynamics simulations, and energy optimizations, a model with two putative active sites could be created and refined. One active site selected to be the most likely one for the docking of oligoprenyl diphosphate and 4-hydroxybenzoic acid is located near the N-terminus of the enzyme. It is widely accepted that residues forming an active site are usually evolutionary conserved within a family of enzymes. Multiple alignments of a multitude of related proteins clearly showed 100% conservation of the amino acid residues that form the first putative active site and therefore strongly support this hypothesis. However, an additional highly conserved region in the amino acid sequence of the ubiA enzyme could be detected, which also can be considered a putative (or rudimentary) active site. This site is characterized by a high sequence similarity to the aforementioned site and may give some hints regarding the evolutionary origin of the ubiA enzyme. Semiempirical quantum mechanical PM3 calculations have been performed to investigate the thermodynamics and kinetics of the catalysis mechanism. These results suggest a near S(N)1 mechanism for the cleavage of the diphosphate ion from the isoprenyl unit. The 4-hydroxybenzoic acid interestingly appears not to be activated as benzoate anion but rather as phenolate anion to allow attack of the isoprenyl cation to the phenolate, which appeared to be the rate limiting step of the whole process according to our quantum chemical calculations. Our models are a basis for developing inhibitors of this enzyme, which is crucial for bacterial aerobic metabolism. [figure: see text]. Structure of the model of ubiA oligoprenyltransferase derived from the photosynthetic reaction center (1PRC). Putative active amino acid residues and substrates are shown as capped sticks to describe their location and geometry in the putative active sites. The violet spheres identify Mg2+.

Molecular Electron Affinities and the Calculation of the Temperature Dependence of the Electron‐Capture Detector Response

AbstractFor Abstract see ChemInform Abstract in Full Text.

Modeling glycosaminoglycans—hyaluronan, chondroitin, chondroitin sulfate A, chondroitin sulfate C and keratan sulfate

Molecular modeling of glycosaminoglycans, hyaluronan, chondroitin, chondroitin-4-sulfate, chondroitin-6-sulfate and keratan sulfate is presented. Semiempirical quantum mechanical calculations, PM3 method, have been used to locate the minimal energy regions in the conformational space around the β 1→3 and β 1→4 glycosidic linkages. The global minima obtained for each of the glycosaminoglycans correspond to a compact conformation across the β 1→3 linkage and to the standard extended form across the β 1→4 linkage. The higher minima obtained around the β 1→3 linkage reproduces the crystallographic data for hyaluronan. A complex of hyaluronan and hydrated chromium ion has been modeled as well (ZINDO method). The complexation at the β 1→3 linkage resulted in an extended conformation.

Synthesis, spectroscopic and crystallographic studies of (1RS,2SR)-1-(2-carboxy-4-methyl-5-methoxyphenyl)-1,2-dimethyl-cyclopentane-2-carboxylic acid: supramolecular framework built from O—H…O and C—H…O hydrogen bonds

Abstract The bicyclic carboxylic acid, C17H22O5, a potential intermediate in the synthesis of bioactive δ-cuparenol has been prepared and characterized by spectroscopic and X-ray studies. The structure derived from the NMR data, the infrared spectra and the chemical analysis is consistent with that of single crystal X-ray analysis. The molecules in the title compound are linked into a three dimensional framework by O—H…O and C—H…O intermolecular hydrogen bonds. The supramolecular assembly of molecules exhibits R4 4(23) rings. The conformational analysis of the molecule as investigated by the semi-empirical quantum mechanical AM1 calculations shows a good agreement with the X-ray structure.

A fluorogenic probe for the copper(I)-catalyzed azide-alkyne ligation reaction: modulation of the fluorescence emission via 3(n,pi)-1(pi,pi) inversion.

Chemoselective ligation reactions represent a powerful approach for labeling of proteins or small molecules in a biological environment. We report here a fluorogenic probe that is activated by click chemistry, a highly versatile bio-orthogonal and chemoselective ligation reaction which is based on the azide moiety as the functional group. The electron-donating properties of the triazole ring that is formed in the course of the coupling reaction was effectively utilized to modulate the fluorescence output of an electronically coupled coumarin fluorophore. Under physiological conditions the probe is essentially nonfluorescent and undergoes a bright emission enhancement upon ligation with an azide. Time-resolved emission spectroscopy and semiempirical quantum-mechanical calculations suggest that the fluorescence switching is due to an inversion of the energy ordering of the emissive 1(pi,pi*) and nonemissive 3(n,pi*) excited states. The rapid kinetics of the ligation reaction render the probe attractive for a wide range of applications in biology, analytical chemistry, or material science.

Multifunctional properties of monodisperse end-functionalized oligophenylenevinylenes

Abstract Novel series of monodisperse, end-functionalized oligophenylenevinylenes (OPVs) containing up to eight phenyl rings have been designed and synthesized by a convergent approach using the stereoselective Wadsworth–Emmons reactions for an investigation of technologically useful functional properties. According to PM3 semiempirical quantum mechanical calculations, the frontier molecular orbitals and the energy gap of an OPV could be shifted or tuned by the functional substituent(s) that are incorporated as end-caps. Our theoretical and experimental evidences have shown that the end-substituents of an oligomer do not affect coplanarity of the pi-conjugated system. It has also been found that the newly synthesized OPVs can exhibit various useful functional properties such as light-emitting properties, photovoltaic effects, third-order nonlinear optical responses, and chemical sensing properties depending on the nature of the end-substituents. In this contribution, the structural factor(s) that can enhance a specific functional property of a molecule or material will be discussed.

New FeII starting materials: preparation, characterisation and structural features of iron halide complexes with alcohol ligands

The new mononuclear [FeCl2(HOPri)4] (1), polymeric [{Cl3Fe(μ-Cl)Fe(HOPri)4}n] (2) and binuclear [I2Fe(μ-I)2Fe(PriOH)4] (3) iron(II) complexes have been synthesized in high yields in propan-2-ol or toluene/propan-2-ol mixtures at room temperature. Magnetic moment measurements, 57Fe Mössbauer spectroscopy data and the results of semi-empirical quantum mechanical calculations confirmed the high-spin configuration of the iron(II) centres, which were shown to be four- and/or six-coordinate by single crystal X-ray diffraction analyses. Intermolecular hydrogen bonding was observed in the solid state structure of 1, intramolecular interactions in 2, while both intra- and intermolecular association was seen in 3. Long iron–(μ-halide) bonds suggest the possibility of complex dissociation in solution and facile ligand substitution in 2 and 3.

New titanium(IV) and vanadium(IV) haloalkoxides: synthetic route and structural characterisation

The novel binuclear titanium(IV) complex [{TiCl(OPri)2(HOPri )}2(m-OPri)2], 1, and the first mononuclear vanadyl(IV) chloroalcoholate [VCl(O)(HOPri)4]Cl, 2, have been prepared from 2:1:1 mixtures of [Ti(OPri)4], KOPri and VCl3. Products were characterised by elemental analysis, FTIR, EPR, NMR and electronic spectroscopies, magnetic susceptibility measurements and single crystal X-ray diffractometry. A third product was found to be polynuclear and to contain both titanium and vanadium. Semi-empirical quantum-mechanical calculations were carried out for the evaluation of the electronic structure of 1.

Inter- and intramolecular hydrogen bond in methyl 2-hydroxy-9H-1-carbazole carboxylate: effect of solvents and acid concentration

The photo-physics of methyl 2-hydroxy-9H-1-carbazazole carboxylate (MPCC) in different solvents and cyclohexane-trifluoroethanol (TFE) mixtures has been studied by means of absorption, fluorescence, fluorescence excitation spectra, time dependence spectrofluoremetery and AM1 semi-empirical quantum mechanical calculations. Only one small Stoke’s shifted fluorescence band is observed under all the environments, indicating that the geometry of the molecule is not changed much on excitation to the first singlet state (S 1) and excited state intramolecular proton transfer (ESIPT) is not viable both in the ground (S 0) and S 1 states at the room temperature. AM1 calculation shows that the ESIPT is still endothermic in S 1 state. Single exponential decay is observed in the fluorescence from MPCC in all the solvents except acetonitrile and methanol. This suggests that in these two solvents, at least two different conformers are present in the S 0 state, whose absorption spectra are not different from each other. Spectral characteristics of MPCC in cyclohexane as a function of TFE have shown a slight blue shift in the λ max ab, decrease in the ε max, red shift in the λ max fl and decrease in the φ fl. This suggests that intermolecular hydrogen bonding is playing a major role in the deactivation of the fluorescence intensity than the intramoleuclar hydrogen bonding (IHB). Spectral properties of MPCC were also studied as a function of acid–base concentrations. p K a values for different prototropic equilibriums were determined in S 0 and S 1 states and discussed.

Synthesis and Electrochemical Properties of Some Lithium Chelatophosphates

Two new lithium chelatophosphates have been synthesized, purified, and characterized, lithium tris[3,4,5,6-tetrafluor-1,2-benzenediolato(2-)--phosphate(1-) and lithium tris[3-fluoro-1,2-benzenediolato(2-)--phosphate(1-). A precursor, the corresponding acid of lithium tris[3,4,5,6-tetrafluor-1,2-benzenediolato(2-)--phosphate(1-), presumably a super acid, shows a hexacoordinated phosphorous in X-ray analysis, when solvated by two diethyl ether molecules. The anodic oxidation limits of benzenechelatoborates and –phosphates are closely related to the energy of the highest occupied molecular orbital from semiempirical quantum-mechanical calculations with the help of QuantumCache and MOPAC 2002, yielding © 2003 The Electrochemical Society. All rights reserved.

Crystal structure and conformation of N, N′-bis (3,5-dichlorosalicylidene)-2-hydroxy 1,3 diamino-2-propan

N, N′-bis(3,5-dichlorosalicylidene)-2-hydroxy-1,3-diamino-2-propan (C 17H 14Cl 4N 2O 3) was synthesized and its crystal structure determined. It crystallizes in the monoclinic space group, C2/ c, with a=29.734(8), b=4.541(1), c=14.694(2) Å, β=115.85(2), R( F 2)=0.048 for 1704 independent reflections. The title compound has a twofold axis passing through the central C9 atom. The intramolecular hydrogen bond occurs between the pairs of atoms N1 and O1 [2.648(5) Å] and the hydrogen atom is essentially being bonded to the nitrogen atom. There is no intermolecular proximity between molecules. Conformations of the title compound were investigated by semi-empirical quantum mechanical AM1 calculations. The optimized geometry of the molecular structure corresponding to the non-planar conformation is the most stable conformation in the theoretical calculations. The results strongly indicate that the minimum energy conformation is primarily determined by non-bonded steric interactions.

Dimethyl 6-methoxy-4abeta-methyl-9-oxo-1,2,3,4,4a,9,10,10abeta-octahydrophenanthrene-1,1-dicarboxylate.

In the title tricyclic keto-diester, C(20)H(24)O(6), a potential intermediate in the synthesis of bioactive podocarpic acid, the outer cyclohexane ring (in a chair conformation) is cis fused to the central cyclohexanone ring (in a half-chair conformation). The conformational analysis of the compound, investigated by semi-empirical quantum mechanical AM1 calculations, shows a good agreement with the X-ray structure, except for the orientation of the methyl, methoxyphenyl and methoxycarbonyl substituents.

Excited state intramolecular proton transfer in 2-(2′-hydroxyphenyl)-1H-imidazo[4,5-c]pyridine: effects of solvents

Excited state intramolecular proton transfer (IPT) reaction in 2-(2′-hyrdoxyphenyl)-1H-imidazo[4,5-c]pyridine in different solvents and mixtures of binary solvents has been studied by means of UV-vis absorption, fluorescence, fluorescence excitation, time correlated single-photon counting fluorescence spectroscopy and using AM1 semi-empirical quantum mechanical calculations. Dual emission from this molecule in organic solvents under the excitation of 310 nm was observed and was ascribed to different species, rotamer a-1 and tautomer T a, formed by the IPT in the excited S 1 state in rotamer a-2. The emission is discussed in terms of a four-state diagram in which the tautomeric form, in the ground state, is only obtained by emission from the excited tautomer and this species quickly converted into more stable species rotamer a-2. The fluorescence quantum yield of the tautomer emission decreases with the increase of polarity and hydrogen bonding nature of the solvents, whereas that of normal band increases under the similar conditions but it starts decreasing after certain composition of the solvent mixtures. Polarity of the solvents plays the major role in decreasing the fluorescence quantum yield of the tautomeric band.

Relevance of the diastereotopic ligation of magnesium atoms of chlorophylls in Photosystem I

The central magnesium (Mg) atoms of natural occurring tetrapyrroles such as chlorophylls (Chls) and bacteriochlorophylls (BChls) are typically five-coordinated, a fact which leads to the formation of diastereoisomers if the Mg–ligand bond is stable on the time scale of the observation method. This possibility has only been briefly addressed before in a CD-study of BChl c aggregates [T.S. Balaban, A.R. Holzwarth, K. Schaffner, J. Mol. Struct. 349 (1995) 183]. On the basis of the chlorophyll–protein complex photosystem I (PSI), which has recently been characterized by single crystal crystallography [P. Jordan, P. Fromme, H.T. Witt, O. Klukas, W. Saenger, N. Krauß, Nature 411 (2001) 909], we find that chlorophyll a molecules are much more frequently bound by the protein matrix from one side ( anti) than the other one ( syn) in a ratio of 82:14, which corresponds to a significant ΔΔ G value of 4.3 kJ/mol. Syn and anti denote the orientation of the Mg–ligand with respect to the 17-propionic acid esterified by phytol. Furthermore, by parallel sequence analysis we find that the binding sites for both syn and anti chlorophylls have been strongly conserved during evolution—a fact which stresses the nonrandom manner in which chlorophylls are bound by the apoprotein in antenna complexes, in order to exert efficiently their light harvesting function and energy funnelling. Most remarkably, all the syn chlorophylls are part of the inner core antenna system. Results from semiempirical quantum mechanical and detailed exciton coupling calculations allow us to speculate on the functional relevance of the diasteretopicity for PSI functioning.

Photoreactivity of vinyl ether/oxirane‐based resin systems

AbstractWe evaluated the reactivity in homopolymerization and as comonomers in dioxirane/polyol visible‐light curable systems the following vinyl ethers (VEs): mono‐, di‐, and tri(ethylene glycol) divinyl ethers (EGDVE, DEGDVE, and TEGDVE, respectively); 1,6‐hexanediol divinyl ether (HDDVE); cyclohexanedimethanol divinyl ether (CHDMDVE); glycidyl vinyl ether (GVE); 4‐(1‐propenyloxymethyl)‐1,3‐dioxolan‐2‐one (POMDO); and 1,4‐butanediol vinyl ether (BDVE). The dioxirane/polyols (80/20) were Cyracure UVR 6105 or ERL 4206 dioxiranes with polytetrahydrofuran [PTHF; number‐average molecular weight (Mn) = 250]. Reactivities were evaluated by photodifferential scanning calorimetry with visible light. For VE homopolymerization, the relative reactivity ranking (based on exotherm peak maximum time) was TEGDVE > EGDVE > DEGDVE > HDDVE > CHDMDVE > BDVE > GVE ≫ POMDO. For VEs in UVR 6105/PTHF, the ranking was GVE > TEGDVE > CHDMDVE > BDVE > EGDVE ≫ DEGDVE = HDDVE = POMDO. In ERL 4206/PTHF, the ranking was: GVE > TEGDVE > BDVE > DEGDVE ≫ HDDVE > EDGDVE ≫ CHDMDVE = POMDO. The incorporation of an electron‐donating reaction promoter, ethyl‐4‐dimethylaminobenzoate, generally shortened induction times and exotherm peak maximum times and increased rate constants for homopolymerizations and ternary polymerizations. Experimentally determined polymerization reactivities were compared with previously reported semiempirical quantum mechanical calculations of activation energies and heats of reaction. The results of laboratory and computational studies for selected compounds were in general agreement. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 314–326, 2002