Theoretical study of the infrared spectrum of 5-phenyl-1,3,4-oxadiazole-2-thiol by using DFT calculations

We have carried out a structural and vibrational study for 5-phenyl-1,3,4-oxadiazole-2-thiol by using the infrared (IR) spectrum and theoretical calculations. For a complete assignment of the compound IR spectrum, density functional theory calculations were combined with Pulay's scaled quantum mechanical force field methodology in order to fit the theoretical wavenumber values to the experimental ones. An agreement between theoretical and available experimental results was found. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants fitting the observed wavenumbers. The results were then used to predict the Raman spectra, for which there are no experimental data. The nature of the benzyl and oxadiazole rings was studied by means of natural bond order and atoms in molecules theory calculations. In addition, the frontier molecular (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) orbitals were analysed and compared with those calculated for the oxadiazole molecule.     

Ab initio vibrational calculations on ara-T molecule: application to analysis of IR and Raman spectra

The FTIR and FT-Raman spectra are reported for the arabinonucleoside ara-T (1-beta-D-arabinofuranosylthymine), which shows antiviral activity. The accurate knowledge of the vibrational modes is a prerequisite for the elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT-Raman spectra of ara-T were recorded from 4000 to 30 cm(-1). A tetradeuterated derivative (deuteration at N3, and hydroxyl groups O'2, O'3, and O'5) was synthesized and the observed isotopic shifts in its spectra were used for the vibrational analysis of ara-T. The theoretical frequencies and the potential energy distribution (PED) of the vibrational modes of ara-T were calculated using the ab initio Hartree-Fock/3-21G method. An assignment of the vibrational spectra of ara-T is proposed considering the scaled PED and the observed band shifts under deuteration. The scaled ab initio frequencies were in reasonable agreement with the experimental data.     

Theoretical study of AlH(2+)n (n=1-7) dications

The structures and stability of 1–7 dications were calculated at the ab initio MP2/aug-cc-pVTZ level of theory. The dications AlH²⁺ 1 and 2 were characterized to be unstable thermodynamically. However, these and the stable dications, 3–7 have considerable kinetic barriers for deprotonation. Each of the structures 3–7 contains one or more two-electron three-center (2e–3c) bonds. Aluminum atoms of these dications carry most of the positive charges, as indicated by NBO charge calculations.Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

Theoretical calculations on a series of dinuclear vanadium and niobium clusters

Electronic structures of chalcogenide-bridged binuclear clusters of vanadium and niobium with the {M₂(μ-Q₂)₂}⁴⁺, {M₂(μ-Q)₂}⁴⁺ and {M₂(μ-Q)(μ-Q)₂}⁴⁺ cores (Q = S, Se, Te) have been studied by density functional theory methods. In the vanadium clusters, the V-V distances are calculated to be in the range of 2.766-3.193 ?, whereas in the niobium clusters the calculated Nb-Nb bond lengths fall in the range of 2.881-3.380 ?, in accordance with the experimentally determined values. The calculated M-M bond distances generally decrease in the order {M₂(μ-Q₂)₂}⁴⁺ > {M₂(μ-Q)₂}⁴⁺ > {M₂(μ-Q)(μ-Q)₂}⁴⁺ (M = V, Nb, Q = S, Se). The calculated enthalpies of formation for the V clusters are higher than for the corresponding Nb clusters. On the other hand, the M₂Q₂ clusters have always higher enthalpies of formation than the M₂Q₃ species, and also (with the exception of M = V, Q = S) higher values of enthalpy of formation than for the M₂Q₄ species. The hardness η of the niobium clusters are higher than that of the vanadium analogs, except for the [V₂S₂(SH₂)₈]⁴⁺ case. The enthalpies ΔH₂₉₈ and the free energies ΔG₂₉₈ for the reactions of hydrogen addition to the [V₂(μ-S₂)₂(H₂O)₈]⁴⁺ and the [Nb₂(μ-S₂)₂(H₂O)₈]⁴⁺ clusters at constant pressure are −121.75 and −59.73 kJ/mol for the vanadium cluster, and 13.97 and 75.15 kJ/mol for the niobium cluster.     

Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior

The structure of a previously calculated transition state (TS) was used to design the [tetrahydro-2-(methylthio)furan-2-yl]methyl phosphate dianion (1) as a new scaffold for transition-state analogs of reactions catalyzed by the inverting glycosyltransferases. This scaffold contains relevant features of the donor and acceptor and represents a new type of potential inhibitors for these enzymes. Available conformational space of 1 was explored using DFT quantum chemical methods by means of two-dimensional potential-energy maps calculated as a function of Phi, Psi, and omega dihedral angles at the B3LYP/6-31+G* level. The calculated potential energy surfaces revealed the existence of several low-energy domains. Structures from these regions were refined at the 6-311++G** level and led to 14 conformers. The stability of conformers is influenced by their environment, and in aqueous solution two conformers dominate the equilibrium. A superposition of calculated conformers with the predicted TS structure revealed that the preferred conformers in solution nicely mimic structural features of the TS. These results imply that 1 has structural properties required to mimic the TS and therefore can be used as a scaffold for further development of TS-analog inhibitors for retaining glycosyltransferases.     

H-bonded complexes between acetylacetone and two molecules of methanol: HF and DFT level study

Five stable H-bonded complexes (supersystems) between acetylacetone and two methanol molecules were investigated at the B3LYP and HF levels of theory using the 6-311G** and 6-11++G** basis sets. The most stable complex was found as the one with the highest relative bonding and interaction energies. All vibrational frequencies resulting from calculations with the 6-311++G** basis set were compared with the recorded IR spectrum of acetylacetone/methanol mixture in a molar ratio 1:2.     

Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures.

For successful ab initio protein structure prediction, a method is needed to identify native-like structures from a set containing both native and non-native protein-like conformations. In this regard, the use of distance geometry has shown promise when accurate inter-residue distances are available. We describe a method by which distance geometry restraints are culled from sets of 500 protein-like conformations for four small helical proteins generated by the method of Simons et al. (1997). A consensus-based approach was applied in which every inter-Calpha distance was measured, and the most frequently occurring distances were used as input restraints for distance geometry. For each protein, a structure with lower coordinate root-mean-square (RMS) error than the mean of the original set was constructed; in three cases the topology of the fold resembled that of the native protein. When the fold sets were filtered for the best scoring conformations with respect to an all-atom knowledge-based scoring function, the remaining subset of 50 structures yielded restraints of higher accuracy. A second round of distance geometry using these restraints resulted in an average coordinate RMS error of 4.38 A.     

A study of the conformations of valinomycin in solution phase

Vibrational absorption and vibrational circular dichroism (VCD) spectra of valinomycin are measured, in different solvents, in the ester and amide carbonyl stretching regions. The influence of cations, namely Li(+), Na(+), K(+), and Cs(+), in methanol-d(4) solvent is also investigated. Ab initio quantum mechanical calculations using density functional theory and 6-31G* basis set are used to predict the absorption and VCD spectra. A bracelet-type structure for valinomycin that reproduces the experimental absorption and VCD spectra in inert solvents is identified. For the structure of valinomycin in polar solvents, a propeller-type structure was optimized, but further investigations are required to confirm this structure. A symmetric octahedral environment for the ester carbonyl groups in the valinomycin-K(+) complex is supported by the experimental VCD spectra. The results obtained in the present study demonstrate that even for large macrocyclic peptides, such as valinomycin, VCD can be used as an independent structural tool for the study of conformations in solution.     

Ab Initio and DFT Study of the Structures,Vibrations and Energetics of the Urea Dimer and Trimer

Stable structures and electronic properties of small urea clusters are investigated with ab initio calculations. We optimized the cluster geometries and calculated the vibrational frequencies with Hartree–Fock (HF), second-order Møller-Plesset perturbation theory (MP2), and Density Functional Theory (DFT) methods using different basis sets. The most stable dimer was found to consist of two nonplanar urea molecules which are connected by two N–-H...O bonds in a common plane, and the most stable trimer has a flat structure of complex and planar C2 form for each urea molecule, like in the crystal. The interaction energies were corrected for the basis set superposition error (BSSE) using the full Boys*ndash;Bernardi counterpoise correction scheme. The stability of different dimer and trimer structures, the features of formation of H-bonds and presented here are compared to the available experimental data.     

Theoretical study on the series of [Au3Cl3M2] complexes, with M = Li, Na, K, Rb, Cs

The prediction of the series of complexes [Au₃Cl₃M₂] with M = Li, Na, K, Rb and Cs, has been achieved at the ab initio level of theory. All geometries were fully optimized at the MP2 level of theory; the central Au₃ cluster is capped by chlorine atoms and the alkaline metals lie above and below the plane of the central ring; aurophilic interactions were found on the metal cluster, and also a strong aromatic character coming from the delocalized d-electrons of the Au atoms according to nuclear independent chemical shift calculations. On the other hand, the chemical hardness parameter was used to test the stability of the series of complexes, and the Fukui indexes of electrophilic and nucleophilic attack were employed to explore possible sites where chemical reactivity may play a role. Figure Molecular representations of the series of complexes [Au₃Cl₃M₂] (M = Li, Na, K, Rb, Cs) and their corresponding chemical hardness     

Ab initio calculations on the thermodynamic properties of azaborospiropentanes

Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies, enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about −52 kJ per gram. Figure Optimized geometry for R-azatriborospiropentane (10) Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ion pair formation involving methylated lysine side chains: A theoretical study

Lysine residues with one, two, or three methyl groups substituted on the ?-nitrogen atom are found in many proteins. To evaluate the effect of the posttranslational methylation on ion-pair formation we have performed semiempirical and ab initio molecular orbital calculations, using the AMI method and the 6-31G^* basis set, respectively. Combinations of various methylated forms of methylamine and ethylamine with formate, acetate, and dimethyl phosphate were studied as model compounds. This approach allowed us to obtain information relevant to the interaction of the modified Lys residues with carboxylate groups of proteins, and the backbone of nucleic acids. We have found that the interaction energy decreases with an increasing number of methyl groups. Inclusion of a solvent reaction field in the semiempirical calculations gave reasonable values for the interaction energy in aqueous solution, when formate and acetate were the counterions. These studies suggest that, in addition to other factors, a weakening of ionic interactions contributes to the various physiological effects of lysine methylation. © 1994 John Wiley & Sons, Inc.     

3-Silaoxetane and 3-silathietane: structure and reactivity studies on the basis of spectroscopic data and theoretical calculations

The ab initio and DFT calculations (structural parameters, electron localization function (ELF)) on 3-silaoxetane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-oxa-3-silacyclobutane (1) and 3-silathietane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-sila-3-thiacyclobutane (2) show the cyclobutane ring in 2 as being non-planar with a C-Si-C angle of 89.2° and a C-S-C angle of 93.3°, whereas the cyclobutane ring in 1 is planar with an unusual small bond angle at the silicon atom of 74.7°, which can only be explained by bent bonds. Since the synthesis was performed in water, small bent angles cannot be indicative for high reactivity. The Raman spectra of 1 and 2 were then recorded and analyzed in the 1800-200 cm⁻¹ spectral region at various temperatures (300-10 K) with the help of the DFT calculation results (harmonic vibrational wavenumbers, Raman scattering activities). Although the wavenumber shifts are quite small, the subtle changes in the spectral features of the 3-silaoxetane and phenyl rings vibrational modes may indicate a loss of symmetry in 1 (between 200 and 150 K) and a possible phase transition in 2 (at about 200 K). Furthermore, the Raman spectra of 1 and 2 confirmed the ELF calculation results, excluding any bond interaction between the silicon and the oxygen or sulfur atom.     

A DFT/ab initio study of hydrogen bonding and conformational preference in model cellobiose analogs using B3LYP/6-311++G**

A series of beta-cellobiose analogs were studied at the B3LYP/6-311++G** level of theory to isolate and understand how the various electronic components of the beta-(1-->4)-linked disaccharide, cellobiose, contribute to the energetic stability of the molecule in vacuo. Previous studies on beta-cellobiose (see accompanying paper) showed that the most energetically stable conformation was that in which the dihedral angle phi (phi(H)) was 'flipped' by approximately 180 degrees relative to the 'normal' form. From our examination of eight sets of structures in which different combinations of functional hydroxyl and hydroxymethyl groups were removed, it was determined that only beta-cellobiose and one other analog (analog 7, beta-xylobioside), an analog in which both hydroxymethyl groups were removed but the exocyclic hydroxyl groups retained, can form a 'cooperative' hydrogen-bonding network. Only in these two molecules did we find continuous synergistic 'communication' through hydrogen bonding from one sugar moiety to the other. This 'cooperative' hydrogen bonding energetically stabilizes the 'flipped' conformation of beta-cellobiose and beta-xylobioside, while the other analogs studied were unable to form a 'cooperative' grouping of hydrogen bonds and thus were more stable in their 'normal' conformational state.     

Molecular mechanic study of nerve agent O-ethyl S-[2-(diisopropylamino)ethyl]methylphosphonothioate (VX) bound to the active site of Torpedo californica acetylcholinesterase

Herein a molecular mechanic study of the interaction of a lethal chemical warfare agent, O-ethyl S-[2-(diisopropylamino)ethyl]methylphosphonothioate (also called VX), with Torpedo californica acetylcholinesterase (TcAChE) is discussed. This compound inhibits the enzyme by phosphonylating the active site serine. The chirality of the phosphorus atom induces an enantiomeric inhibitory effect resulting in an enhanced anticholinesterasic activity of the S_P isomer (VX^S) versus its R_P counterpart (VX^R). As formation of the enzyme-inhibitor Michaelis complex is known to be a crucial step in the inhibitory pathway, this complex was addressed by stochastic boundary molecular dynamics and quantum mechanical calculations. For this purpose two models of interaction were analyzed: in the first, the leaving group of VX was oriented toward the anionic subsite of TcAChE, in a similar way as it has been suggested for the natural substrate acetylcholine; in the second, it was oriented toward the gorge entrance, placing the active site serine in a suitable position for a backside attack on the phosphorus atom. This last model was consistent with experimental data related to the high inhibitory effect of this compound and the difference in activity observed for the two enantiomers. Proteins 28:543–555, 1997. © 1997 Wiley-Liss, Inc.     

Formation and temperature stability of G-quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations

Variations in the structure of d(GGGA)(5) oligonucleotide in the presence of Li(+), Na(+), and K(+) ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3-Lee-Yang-Parr functional at the 6-31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)(5) in the presence of Li(+) forms a nonplanar single tetramer, with angles of 102 degrees and 171 degrees between neighboring guanine bases. This tetramer changes its geometry at temperatures >50 degrees C, but does not form a quadruplex structure. In the presence of Na(+), the d(GGGA)(5) structure was optimized to almost planar tetramers with an angle of 177 degrees between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60 degrees C. The Hartree-Fock energies imply that d(GGGA)(5) prefers to form complexes with Na(+) rather than Li(+). The d(GGGA)(5) structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li(+) < Na(+) < K(+).     

Oxoselenide triangular molybdenum clusters: Synthesis and characterization of [Mo3SeO3(acac)3(py)3]PF6

New cluster complex [Mo₃SeO₃(acac)₃(py)₃]⁺ was obtained by ligand substitution in the aqua complex [Mo₃SeO₃(H₂O)₉]⁴⁺. Crystal structure was determined for [Mo₃SeO₃(acac)₃(py)₃]PF₆·C₆H₅CH₃. The complex was characterized by ⁷⁷Se NMR, electrospray mass-spectrometry, and cyclic voltammetry. DFT calculations were used to confirm the assignment of chemical shift and to study Mo-Mo bonding in the cluster core.