An improved generalized AMBER force field (GAFF) for urea

We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.     

Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers

The conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point.     

Formation of the Vilsmeier-Haack complex: the performance of different levels of theory

Because of discrepancies in the available experimental data, an extensive theoretical investigation of the formation of the Vilsmeier-Haack (VH) complex has been carried out. The barriers to complex formation calculated using eight different density functional methods (BLYP, B2-PLYP, B3LYP, B3PW91, MPW1K, M06-2X, and PBE1PBE), MP2, and extrapolation techniques (CBS-QB3, G3B3) with several basis sets (6 − 31 + G**, 6 − 311++G**, 6 − 311 + (3df,2p), aug-cc-pVDZ, and aug-cc-pVTZ) were compared with experimental data. For the overall reaction, MP2/aug-cc-pVDZ and M06-2X/6−31 + G(d,p) perform best compared to the CBS techniques. The results help clarify some open mechanistic questions.     

Quantum-chemical investigation of the structure and the antioxidant properties of α-lipoic acid and its metabolites

Quantum-chemical computations were used to investigate the structure-antioxidant parameter relationships of α-lipoic acid and its natural metabolites bisnorlipoic acid and tetranorlipoic acid in their oxidized and reduced forms. The enantiomers of lipoic and dihydrolipoic acid were optimized using the B3LYP/6-311+G(3df,2p), B3LYP/aug-cc-pVDZ and MP2(full)/6-31+G(d,p) levels of theory as isolated molecules and in the presence of water. The geometries of the metabolites and the values of their antioxidant parameters (proton affinity, bond dissociation enthalpy, adiabatic ionization potential, spin density, and the highest occupied molecular orbital energy) were calculated at the B3LYP/6-311+G(3df,2p) level of theory. The results obtained reveal similarities between these structures: a pentatomic, nonaromatic ring is present in the oxidized forms, while an unbranched aliphatic chain (as found in saturated fatty acids) is present in both the oxidized and the reduced forms. Analysis of the spin density and the highest occupied molecular orbital energy revealed that the SH groups exhibited the greatest electron-donating activities. The values obtained for the proton affinity, bond dissociation enthalpy and adiabatic ionization potential indicate that the preferred antioxidant mechanisms for α-lipoic acid and its metabolites are sequential proton loss electron transfer in polar media and hydrogen atom transfer in vacuum.     

On the protonation equilibrium for the benzimidazole derivative Hoechst 33258: an electronic molecular orbital study

Hoechst 33258 and its deprotonated forms have been examined in the gas-phase and in solution using quantum mechanical methods. Ab initio calculations at the HF level have been used to investigate the more relevant geometrical trends of such species, while proton affinities and gas-phase basicities were derived from B3LYP and MP2 electronic energies. Solvation energies were calculated using a dielectric continuum model: MST. The Delta(p)K(a) values were estimated by combining the gas-phase basicities and the free energies of solvation. Comparison of these Delta(p)K(a) values with experimentally reported data have been used to highlight the advantages and limitations of this strategy.     

Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers

Dipole moments (μ), charge distributions, and static electronic first-order hyperpolarizabilities (β _μ ) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree–Fock, Møller–Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning’s correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a μ value smaller than that of the 9H form by a factor of ca. 3.5. The β _μ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the β _μ (9H)/β _μ (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the β _μ values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.

A B3LYP and MP2 theoretical investigation into host-guest interaction between calix[4]arene and Li+ or Na+

The DFT-B3LYP and MP2 methods with 6-311G** and 6-311++G** basis sets have been applied to study the complexation energies of the host-guest complexes between the cone calix[4]arene and Li⁺ or Na⁺ on the B3LYP optimized geometries. A comparison of the complexation energies obtained from the MP2(full) with those from MP2(fc) method is also carried out. The result shows that it is essential to introduce the diffuse basis set into the geometry optimizations and complexation energy calculations of the alkali-metal cation-π interaction complexes of calix[4]arene, and the D _e values show a maximum of 21.13 kJ mol⁻¹ (14.45% of relative error) between the MP2(full)/6-311++G** and MP2(fc)/6-311++G** method. For Li⁺ cation, the complexation is mainly energetically stabilized by the lower rim/cation (namely O–Li⁺) interaction. However, binding energies and NBO analyses confirm that Na⁺ cation prefers to enter the calix[4]arene cavity and the cation-π interaction is predominant, which contradicts the previous low-level theoretical studies. Furthermore, the complexation with Li⁺ is preferred over that with Na⁺ by at least 12.70 kJ mol⁻¹ at MP2(full)/6-311++G**//B3LYP/6-311++G** level.      

Interference of H-bonding and substituent effects in nitro- and hydroxy-substituted salicylaldehydes

Two intramolecular interactions, i.e., (1) hydrogen bond and (2) substituent effect, were analyzed and compared. For this purpose, the geometry of 4- and 5-X-substituted salicylaldehyde derivatives (X = NO₂, H or OH) was optimized by means of B3LYP/6-311 + G(d,p) and MP2/aug-cc-pVDZ methods. The results obtained allowed us to show that substituents (NO₂ or OH) in the para or meta position with respect to either OH or CHO in H-bonded systems interact more strongly than in the case of di-substituted species: 4- and 3-nitrophenol or 4- and 3-hydroxybenzaldehyde by ∼31%. The substituent effect due to the intramolecular charge transfer from the para-counter substituent (NO₂) to the proton-donating group (OH) is ∼35% greater than for the interaction of para-OH with the proton-accepting group (CHO). The total energy of H-bonding for salicylaldehyde, and its derivatives, is composed of two contributions: ∼80% from the energy of H-bond formation and ∼20% from the energy associated with reorganization of the electron structure of the systems in question.     

Theoretical 49Ti NMR chemical shifts

⁴⁹Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6–31G(d)//B3LYP/6–31G(d) proves to give very good agreement with experimental data over a range from 1,400 to −1,300 ppm. The MP2/6–31G(d)//MP2/6–31G(d) level computes even smaller average deviations but fails for TiI₄. This behavior together with its huge demand for computational resources requires careful handling of this theoretical level. In addition, NMR data for five titanium fulvene (or related) complexes are given. Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

Many-body energies during proton transfer in an aqueous system

The energetics of the mechanism of proton transfer from a hydronium ion to one of the water molecules in its first solvation shell are studied using density functional theory and the Møller–Plesset perturbation (MP2) method. The potential energy surface of the proton transfer mechanism is obtained at the B3LYP and MP2 levels with the 6-311++G** basis set. Many-body analysis is applied to the proton transfer mechanism to obtain the change in relaxation energy, two-body, three-body and four-body energies when proton transfer occurs from the hydronium ion to one of the water molecules in its first solvation shell. It is observed that the binding energy (BE) of the complex decreases during the proton transfer process at both levels of theory. During the proton transfer process, the % contribution of the total two-body energy to the binding energy of the complex increases from 62.9 to 68.09% (39.9 to 45.95%), and that of the total three-body increases from 25.9 to 27.09% (24.16 to 26.17%) at the B3LYP/6-311++G** (MP2/ 6-311++G**) level. There is almost no change in the water–water–water three-body interaction energy during the proton transfer process at both levels of theory. The contribution of the relaxation energy and the total four-body energy to the binding energy of the complex is greater at the MP2 level than at the B3LYP level. Significant differences are found between the relaxation energies, the hydronium–water interaction energies and the four-body interaction energies at the B3LYP and MP2 levels.     

DFT study of a substrate and inhibitors of 1-deoxy-2-xylulose-5-phosphate reductoisomerase – the potential novel target molecule for anti-malaria drug development

1-Deoxy-2-xylulose-5-phosphate (DOXP) reductoisomerase is a novel target for developing anti-malaria drugs. The determination of structural and electronic properties of the inhibitor molecules is of crucial importance for analyzing the interactions between DOXP-reductoisomerase and its inhibitors. Geometry-optimizations and single point calculations at the B3LYP/3-21G*//B3LYP/3-21G** and B3LYP/3-21G*//MP2/3-21G** levels were performed to determine the structures and charge distributions of an enzyme substrate (1-deoxy-D-xylulose 5-phosphate) and the two inhibitors (fosmidomycin and FR-900098). The theoretically derived bond lengths are in excellent agreement with the corresponding experimental values reported for similar structures. Partial charges and dipole moments are assigned using the Mulliken and natural population analyses. The calculated structures and partial charge distributions can readily be used for the further development of biologically active inhibitors of DOXP-reductoisomerase as well as parameters for docking experiments.Electronic Supplementary Material available.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

Ab initio study of phenyl benzoate: structure,conformational analysis,dipole moment,IR and Raman vibrational spectra

The molecular structure (bond distances and angles), conformational properties, dipole moment and vibrational spectroscopic data (vibrational frequencies, IR and Raman intensities) of phenyl benzoate were calculated using Hartree–Fock (HF), density functional (DFT), and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6-31G* to 6-311++G**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2, B3LYP and B3PW91 levels with basis sets including diffuse functions. The B3LYP/6-31+G* theory level estimates the shape of the experimental functions for phenyl torsion around the Ph–O and Ph–C bonds well, but reproduces the height of the rotational barriers poorly. The B3LYP/6-31+G* harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported. They are in excellent agreement with experimental IR and Raman spectra.Figure Calculated and experimental (GED) potential energy functions for torsional motion of phenyl benzoate relative to the minimum value. a The potential function for torsion about the O₃–C₄ bond. b The potential function for torsion about the C₂–C₁₀ bond.     

Nitrosation of malononitrile by HONO,ClNO and N<Subscript>2</Subscript>O<Subscript>3</Subscript>: A theoretical study

Nitrosation reactions of malononitrile by three nitrosating agents, HONO, ClNO, and N₂O₃, have been theoretically investigated at the B3LYP/cc-pVTZ and MP2/cc-pVDZ levels. Two possible competitive paths for nitrosation of malononitrile to give 2-nitroso-malononitrile were proposed: (a) direct C-nitrosation and (b) N-nitrosation and subsequent nitroso transfer from N to C atom. The calculations show that at both B3LYP and MP2 levels, path b is kinetically favored over path a for nitrosations by HONO and N₂O₃. In the case of ClNO, the B3LYP predicts preference of path b, while the MP2 calculations suggest that both paths have similar rate-determining barriers. The data suggest that N₂O₃ is the preferred nitrosating agent for the nitrosation of malononitrile in aqueous solution. Transformation of 2-nitroso-malononitrile to form malononitrileoxime via intramolecular proton transfer has also been explored, and it is found that inclusion of an assistant water molecule can drastically accelerate the tautomerization.     

Noble gas inserted compounds of borazine and its derivative B<Subscript>3</Subscript>N<Subscript>3</Subscript>R<Subscript>6</Subscript>: structures and bonding

Quantum chemistry computations were performed at the MP2 and B3LYP levels of theory using the basis sets aug-cc-pVDZ and def2-TZVPPD to study the noble gas (Ng) compounds formed by insertion of a Ng atom (Kr, Xe, Rn) into the B–H/F and N–H/F bonds of inorganic benzene B₃N₃H₆ and its fluorine derivative B₃N₃F₆. The geometrical structures were optimized and vibrational analysis was carried out to demonstrate these structures being local minima on the potential energy surface. The thermodynamic properties of the formation process of Ng compounds were calculated. A series of theoretical methods based on the wavefunction analysis, including NBO, AIM and ELF methods and energy decomposition analysis, was used to investigate the bonding nature of the noble gas atoms and the properties of the Ng compounds. The N–Ng bond was found to be stronger than the B–Ng bond, but the B–Ng bond is of typical covalent character and σ-donation from the Ng atom to the ring B atom makes the predominant contribution towards stability of the B-Ng bond. NICS calculation shows that these Ng-containing compounds are of weak π-aromaticity.     

Mechanistic investigation of the base-promoted cycloselenoetherification of pent-4-en-1-ol

The mechanism of phenylselenoetherification of pent-4-en-1-ol using some bases (pyridine, triethylamine, quinoline, 2,2′-bipyridine) as catalyst was examined through studies of kinetics of the cyclization, by UV-VIS spectrophotometry. It was demonstrated that the intramolecular cyclization is facilitated in the presence of bases caused by the hydrogen bond between base and alkenol’s OH-group. The obtained values for rate constants have shown that the reaction with triethylamine is the fastest one. Quantum chemical calculations (MP2(fc)/6-311+G**//B3LYP/6-311+G**) show, that the transition state of the cyclisation is S_N2 like.     

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.03 A less, compared to B3LYP method. MP2 calculation and single point CCSD(T)//MP2 calculation have been considered to decompose the interaction energy, including corrections for basis set superposition error (BSSE). Moreover, charge distribution analysis has also been carried out to understand the long raised questions, how and why the two body energies have significant contribution to the total binding energy.     

Ab Initio Quantum Mechanics Analysis of Imidazole C-H…O Water Hydrogen Bonding and a Molecular Mechanics Forcefield Correction

Abstract

While it is well established that classical hydrogen bonds play an important role in enzyme structure, function and dynamics, the role of weaker, but ‘activated’ C-H donor hydrogen bonds is poorly understood. The most important such case involves histidine which often plays a direct role in enzyme catalysis and possesses the most acidic C-H donor group of the standard amino acids. In the present study, we obtained optimized geometries and hydrogen bond interaction energies for C-H…O hydrogen bonded complexes between methane, ethylene, benzene, acetylene, and imidazole with water at the MP2-FC/6-31++G(2d,2p) and MP2-FC/aug-cc-pVDZ//MP2-FC/6-31++G(2d,2p) levels of theory. A strong linear relationship is obtained between the stability of the various hydrogen bonded complexes and both separation distances for H…0 and C—O. In general, these calculations indicate that C-H…0 interactions can be classified as hydrogen bonding interactions, albeit significantly weaker than the classical hydrogen bonds, but significantly stronger than just van der Waals interactions. For instance, while the electronic energy of stabilization at the MP2-FC/aug-cc-pVDZ//MP2-FC/6-31++G(2d,2p) level of theory of a water C-H…O water hydrogen bond is 4.36 kcal/mol more stable than the methane C-H…O water interaction, the water-water hydrogen bond is only 2.06 kcal/mol more stable than the imidazole C_e?H…O water hydrogen bond. Neglecting this latter hydrogen bonding interaction is obviously unacceptable. We next compare the potential energy surfaces for the imidazole C_e?H…O water and imidazole N_d?H…O hydrogen bonded complexes computed at the MP2/6-31++G(2d,2p) level of theory with the potential energy surface computed using the AMBER molecular mechanics program and forcefields. While the Weiner et al and Cornell et al AMBER forcefields reasonably account for the imidazole N-H…O water interaction, these forcefields do not adequately account for the imidazole C_e?H…O water hydrogen bond. A forcefield modification is offered that results in excellent agreement between the ab initio and molecular mechanics geometry and energy for this C-H…O hydrogen bonded complex.     

Theoretical potential scans and vibrational spectra of vinyl selenonyl halides CH2=CH–SeO2X (X is F, Cl and Br)

The structure and conformational stability of vinyl selenonyl fluoride, chloride and bromide CH₂=CH–SeO₂X (X is F, Cl and Br) were investigated using density functional B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. From the calculations the molecules were predicted to exist only in the non-planar gauche conformation with the vinyl C=C group almost eclipsing one of the selenonyl Se=O bonds as a result of conjugation between the two moieties. Single-minimum potential scans were calculated at the DFT level for the molecules. The vibrational frequencies were computed using B3LYP/6-311+G**. Normal coordinate calculations were then carried out and potential energy distributions were calculated for the three molecules in the gauche conformation.Figure Potential function for the asymmetric torsion in vinyl selenonyl fluoride (dotted line), chloride (dashed line) and bromide (solid line) as determined at the DFT-B3LYP/6-311+G** level