Journal of Theoretical and Computational Chemistry

The M05-class (M05 and M05-2X) and M06-class (M06, M06-2X, M06-HF, and M06-L) functionals, developed by Zhao and Truhlar, have shown better performance than popular older DFT functionals in obtaining accurate binding energies of noncovalent complexes. However, the reliability of these functionals for the structure and geometry of noncovalent systems was seldom assessed. Here, using the MP2/aug-cc-pVTZ values as a benchmark, we assessed the performance of the M05-class and M06-class functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes. The results clearly show that the M05, M06 and M06L functionals totally fail to predict the structure of the hydrogen-bonded complex formed between glycine and carbonic acid whereas the M05-2X, M06-2X, M06-HF, and even B3LYP succeed. For the geometries of a series of halogen-bonded complexes, it is found that the M05-2X functional performs slightly better than the M06-2X and M06-HF functionals and much better than the M05, M06 and M06-L functionals on average. Based on these tests, we concluded that the M05, M06 and M06-L functionals are not good for the study of the structure and geometry of the hydrogen-bonded and halogen-bonded complexes and the density functional M05-2X is the best choice. In addition, we have also assessed the integration grid errors arising from the numerical integration of these functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes.

We report averaged potential energy surfaces for isotopic Ne–CO₂ complexes (²⁰Ne–¹³C¹⁶O₂, ²²Ne–¹²C¹⁶O₂ and ²²Ne–¹³C¹⁶O₂). According to the latest ab initio potential of ²⁰Ne–¹²C¹⁶O₂ (Chen R, Jiao EQ, Zhu H, Xie DQ, J Chem Phys133:104302, 2010) including the Q₃ normal mode for the υ₃ antisymmetric stretching vibration of the CO₂ molecule. We obtain the averaged potentials for ²⁰Ne–¹³C¹⁶O₂, ²²Ne–¹²C¹⁶O₂ and ²²Ne–¹³C¹⁶O₂ by the integration of the three-dimensional potential over the Q₃ coordinate. The averaged potential surfaces are found to have a T-shaped global minimum and two equivalent linear local minima. The radial DVR/angular FBR method and the Lanczos algorithm are applied to calculate the rovibrational energy levels. Comparison with the available observed values showed an overall excellent agreement for all spectroscopic parameters and the microwave spectra.

The interactions of the four typical nucleotides with the metal ions Mg²⁺, Ca²⁺, Mn²⁺, Na⁺, and K⁺ were studied by using the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) calculations in the PCM model. A lot of initial binding sites of the metal ions were designed and optimized to determine the most stable structures of the metal ion nucleotide compounds. It has been shown that the metal ions tend to attach at the center of the negatively charged atoms of the nucleotides. Furthermore, the vertical excitation energies of the metal ion nucleotide compounds were calculated at the same level with the TDDFT method, and also NBO charges were analyzed to understand the bonding characteristics between the metal ions and the nucleotides. That was also compared with the conclusion in the gas phase.

We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece and 56-residue E-domain of Staphylococcal protein A, by combining molecular dynamics (MD) simulations with Coarse-Grained United-Residue (UNRES) Force Field and all-atom force field. Starting from extended structures, each of the proteins was folded to a stable structure within a short time frame using the UNRES model. However, the secondary structures of helices were not well formed. Further refinement using MD simulations with the all-atom force field was able to fold the protein structure into the native-like state with the smallest main-chain root-mean-square deviation of around 3 Å. Detailed analysis of the folding trajectories was presented and the performance of GPU-based MD simulations was also discussed.

The hyperconjugation effect on molecular structural stability is studied by performing first-principles calculations on the tert-butyl and its derived C₄H_n(n = 4–10) isomer structures. Four of the isomer structures with n = 7–10 were found to show hyperconjugation similar to that in the tert-butyl, with hyperconjugation orbital energies decreasing with the increase of the number of hydrogen atoms participating in the hyperconjugation (PIH). The distribution of charge carried by the PIH hydrogen atoms is uniform, which reveals a delocalization character in the electronic structures; and the PIH hydrogen atoms are found responsible for the main IR spectrum peak relating to C-H stretching vibration.

Two diastereoisomers of 2′-acetyloxy-2′-phenylspiro[indeno[1,2-b]quinoxalin-11,1′-cyclopropane] were synthesized and their ¹H NMR spectra were recorded. Their chemical structures were fully optimized at B3LYP/6-311+G(d,p) level of theory using the Gaussian 03W program package. The ¹H NMR chemical shifts were calculated for geometry-optimized structures of the diastereoisomers with the gauge independent atomic orbital (GIAO) and B3LYP method with the 6-311+G(d,p), 6-311++G(d), 6-31++G(d,p) and 6-31+G(d) basis sets. The computational results were then compared with the experimental values and the structures associated with each spectrum were assigned.

Hydrogen bond interactions in biological systems are important scientific issues but are challenging for their theoretical determinations at quantum-mechanical level of theory. Due to the different approximations, the available theoretical approaches often predict diverse hydrogen bond lengths and strengths. In this work, we evaluated the reliabilities of a number of widely used theoretical approaches including HF, SVWN, BLYP, PW91, B3LYP, BH and HLYP, B97D, M06L, MP2, and DFTB-D in studying hydrogen bonding, by calculating the hydrogen bond lengths and binding energies of 23 dimers formed by HCOOH, NH₃ and Glycine. We also compared the effects of STO-3G, 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results. Our result shows that, M06L, B3LYP and BHandHLYP methods can predict accurate dimer structures with a moderate basis set. Moreover, DFTB-D also gives reasonably reliable results with high efficiency and satisfactory precision, being a good choice for studying complex structures which contain hydrogen bonds.

Geometric and electronic properties and vacancy formation energies for two kinds of oxygen-vacancy Cu₂O (111) surfaces have been investigated by first-principles calculations. Results show that the relaxation happens mainly on the top three trilayers of surfaces. Two vacancies trap electrons of -0.11e and -0.27e, respectively. The effects of oxygen vacancies on the electronic structures are found rather localized. The electronic structures suggest that the oxygen vacancies enhance the electron donating ability of the surfaces to some extent. The energies of 1.75 and 1.43 eV for the formation of oxygen vacancies are rather low, which indicates the partially reduced surfaces are stable and easy to produce.

Some low-lying states of the nine-valence-electron systems HBeP^- and HPBe^- anions have been studied for the first time using three methods CASSCF, CASPT2 and B3LYP with the contracted atomic natural orbital (ANO) and cc-pVTZ basis sets. The geometries of all stationary points along the potential energy surfaces were optimized at the CASSCF/ANO, CASPT2/ANO and B3LYP/cc-pVTZ levels. The potential energy curves of isomerization reactions between HBeP^- and HPBe^- were calculated as a function of HBeP bond angle. The ground and the first excited states of HBeP^- are predicted to be X²Π and A²Σ⁺ states, respectively. The X²Σ⁺ and A²Π states of the linear HPBe^- are both first-order saddle points because they have unique imaginary frequency. Two bent minima M1 and M2 were found along the 1²A′ and 1²A″ potential energy surfaces, respectively. The calculated results indicated that the ground-state HBeP^- is linear, while the ground-state HPBe^- is bent.

To provide useful information on dissociation of water molecule on (TiO₂)_n clusters for experimental verification, we have calculated the infrared (IR) and Raman spectra of three possible states involved, namely molecularly adsorbed state, metastable state and dissociatively adsorbed state, using density functional theory at the B3LYP/6-311G(d) level. We find that the characteristic bands of H₂O molecules below 2000 cm^-1 in both IR and Raman spectra vanish upon both molecular and dissociative adsorption of H₂O. In the high frequency range of 3600–4200 cm^-1, the adsorption caused the single IR peak of water to split into two bands, while the dissociation removed the one at lower frequency and blue shifted slightly the higher frequency band. The two Raman peaks of the water molecule in the same high frequency range were slightly blue shifted upon adsorption but the one at lower frequency was removed upon dissociation, while the one at high frequency blue shifted slightly. The intensities of vibrational modes of water in 3600–4200 cm^-1 are generally significantly enhanced upon both molecular and dissociative adsorption. Our results show clearly signatures of dissociation of water molecule into hydroxyl radical at the terminal site.

Based on the DMBE potential surface of the ⁴A″ ground-state, the product rotational polarizations in the title reaction are studied by using quasiclassical trajectory (QCT) calculation method. Three angular distributions of P(θ_r), P(Φ_r), P(θ_r, Φ_r) and the four polarization-dependent differential cross sections (PDDCSs) were calculated for the collision energy range of 1–20 kcal/mol. The results revealed that the product is backward-scattering and the product rotational angular momentum j′ is aligned and oriented. With the increment of collision energy, the degree of the product alignment and orientation is enhanced, showing the collision energy-dependent behaviors of the product polarizations.

Ab initio method is used to figure out the structures and photo-physical processes of 2-aryl substituted indoles, 2-phenylindole (2PI), 2-naphthylindole (2NI), and 2-anthracenylindole (2AI), synthesized experimentally with strong fluorescence. The results show that the photoabsorption and fluorescence measured experimentally correspond to the monovalent anions deprotonated in the indole NH end, other than the neutral compounds. During the photochemical reaction, the angles between the planes of the indole and 2-aryl substituted moieties keep unchanged, but the photo-induced intramolecular charge transfer can immediately occur in the anions. Furthermore, the photo-physical processes after photoexcitation are analyzed by using a linear reaction coordinate.

We investigate theoretically the preparation of ultracold photoassociated Cs₂ molecules in the lowest vibrational level of the ground electronic state via the stimulated Raman adiabatic passage (STIRAP) by solving the time-dependent Schrödinger equation using the mapped Fourier grid method. A negative chirped laser pulse is used to produce the unstable photoassociated molecules in the excited electronic state. A dump pulse is utilized to transfer a partial population of the unstable photoassociated molecules to the vibrational v″ = 18 level of the ground electronic state. This part of population is then transferred to the v″ = 0 level of the ground electronic state by the pump and Stokes laser pulses via an intermediate state which is taken to be the v′ = 7 level of the excited electronic state, forming the stable photoassociated molecules. The population transfer efficiency from v″ = 18 to v″ = 0 in the ground electronic state reaches 96.2% via the STIRAP.

The relative aromaticity of some N-phenylacetamide (NPA) derivatives were investigated in which the NPA was substituted by NO₂, CN, CF₃, Br, Cl, F, H, CH₃, and NH₂ groups at two meta and para positions. For this purpose, density functional theory calculations were applied at the B3LYP/6-31+G(d,p) level to calculate the aromaticity indices including nucleus independent chemical shift (NICS), harmonic oscillator model of aromaticity (HOMA) and harmonic oscillator model of electron delocalization (HOMED). The obtained results indicated that the aromaticity of derivatives decreased in the order of NO₂ > CN > CF₃ > Br > Cl > F > H > CH₃ > NH₂ for both meta and para positions. Furthermore, the resulting order was directly related to the electron withdrawing and electron releasing strengths of the substituents. Finally, it was found that all the aromaticity indices of have a good correlation with the Hammett constant.

The constrained density functional theory (CDFT) was used to study bridge-mediated electron transfer processes in mixed-valence systems with two identical metallocene (cobaltocene, ruthenocene, and nickelocene) moieties linked by various bridge structures. Based on the electronic coupling matrix elements obtained from the CDFT calculations, the relationship between the bridge linkage and the effectiveness of intervalence transfer was discussed.

Neocarzinostatin (NCS) is an antitumor chromophore carrier protein with many applications in clinical use such as drug delivery system; however, so far its chromophore-releasing mechanism remains unclear. In this contribution the process and pathway of the chromophore releasing from holoprotein are revealed by conventional molecular dynamics simulations and essential dynamics (ED) sampling method. The results are consistent with the model for ligand release proposed in [D. H. Chin et al., J Biol Chem281:16025, 2006]. The further analysis suggests that the conformational changes of loop 99–104 and motions of side-chain of residue Phe78 are important factors for chromophore release; the opening state of loop 99–104 is a precondition for the release of ligand.