Ruo-Zhuang Liu

Photodissociation of formic acid

The photodissociation of formic acid has been studied experimentally and theoretically. Ab initio calculations were performed to study the dissociative profiles of five reaction channels on the S0, S1, and T1 potential energy surfaces. The vibrationally excited nascent products were detected using a time-resolved Fourier transform infrared spectrometer after laser photolysis at 248 or 193 nm. In the 248 nm photolysis, the HCOOH molecule was first excited to the S1 state, but it was found that the dissociation takes place on the S0 surface after internal conversion. The products of the vibrationally excited CO, CO2(v3) and H2O(v1) were detected. During the dissociation process the vibrationally energized molecule is geometrically memorized and dynamically controlled, with the yield preference of CO and H2O over that of CO2 and H2. The ratio of CO(v⩾1)/CO2(v⩾1) is estimated as <7.5. Vibrationally excited CO (v) and CO2(v3) are also found in the 193 nm photolysis but the CO/CO2 ratio increases to 11. Most of...

The infrared spectrum of the nitric oxide dimer cation: Problems for density functional theory and a muddled relationship to experiment

Ab initio and density functional theory (DFT) methods have been used to study the geometries, vibrational frequencies, and infrared intensities for the trans-, cis-, and gauche-structures of the ONNO+ cation. Five different functionals were employed for comparison. Double-ζ plus polarization (DZP) basis sets and triple-ζ plus double polarization with f functions (TZ2Pf) basis sets were utilized. The ground state of the trans-ONNO cation is of 2Ag symmetry. The prominent infrared absorption is predicted as ∼1900 cm−1 based upon the DFT methods. However, this DFT prediction is suspect since ONNO+ exhibits inverse symmetry breaking, dissociating to the physically absurd limit ON+1/2 plus NO+1/2. This inverse symmetry breaking phenomenon was discussed in an important 1997 paper by Bally and Sastry [J. Phys. Chem. A 101, 7923 (1997)]. Therefore, a higher theoretical level, Brueckner coupled-cluster method was ultimately applied, and the harmonic vibrational frequency of this mode was predicted to be about 1550...

Theoretical studies on pyridoxal 5′‐phosphate‐dependent transamination of α‐amino acids

Density functional methods have been applied to investigate the irreversible transamination between glyoxylic acid and pyridoxamine analog and the catalytic mechanism for the critical [1,3] proton transfer step in aspartate aminotransferase (AATase). The results indicate that the catalytic effect of pyridoxal 5′‐phosphate (PLP) may be attributed to its ability to stabilize related transition states through structural resonance. Additionally, the PLP hydroxyl group and the carboxylic group of the amino acid can shuttle proton, thereby lowering the barrier. The rate‐limiting step is the tautomeric conversion of the aldimine to ketimine by [1,3] proton transfer, with a barrier of 36.3 kcal/mol in water solvent. A quantum chemical model consisting 142 atoms was constructed based on the crystal structure of the native AATase complex with the product L‐glutamate. The electron‐withdrawing stabilization by various residues, involving Arg386, Tyr225, Asp222, Asn194, and peptide backbone, enhances the carbon acidity of 4′‐C of PLP and Cα of amino acid. The calculations support the proposed proton transfer mechanism in which Lys258 acts as a base to shuttle a proton from the 4′‐C of PLP to Cα of amino acid. The first step (proton transfer from 4′‐C to lysine) is shown to be the rate‐limiting step. Furthermore, we provided an explanation for the reversibility and specificity of the transamination in AATase.

DFT Study on the Mechanism of Escherichia coli Inorganic Pyrophosphatase

Escherichia coli inorganic pyrophosphatase (E-PPase) is a tetranuclear divalent metal dependent enzyme that catalyzes the reversible interconversion of pyrophosphate (PPi) and orthophosphate (Pi), with Mg(2+) conferring the highest activity. In the present work, the reaction mechanism of E-PPase is investigated using the hybrid density functional theory (DFT) method B3LYP with a large model of the active site. Our calculated results shed further light on the detailed reaction mechanism. In particular, the important residue Asp67, either protonated or unprotonated, was taken into account in the present calculations. Our calculations indicated that a protonated Asp67 is crucial for the reverse reaction to take place; however, it is lost sight of in the forward reaction. The bridging hydroxide is shown to be capable of performing nucleophilic in-line attack on the substrate from its bridging position in the presence of four Mg(2+) ions. During the catalysis, the roles of the four magnesium ions are suggested to provide a necessary conformation of the active site, facilitate the nucleophile formation and substrate orientation, and stabilize the trigonal bipyramid transition state, thereby lowering the barrier for the nucleophilic attack.

Theoretical investigation of the self-assembly of cyclo[(-β3-HGly)4-]

Abstract Cyclo[(-β3-HGly)4-] and its oligomers were studied using the density function B3LYP method. Their energetics and structural characteristics were calculated and analyzed. Significantly, we observed that the average interaction energy between two adjacent monomers in the β3-cyclopeptide oligomers showed marked increase upon addition of more monomers. However, the enhancement will gradually become weaker and eventually reach a plateau, giving rise to a stable nanotube. The same phenomenon was observed for their geometric structures and dipole moments of the assembly. Based on these new insights, we suggest that the synergetic effect resulted from addition of monomers will facilitate the enhancement of favorable interaction of the nanotube, which is the primary driving force of self-assembly.

DFT study of the asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex.

We report the mechanism of asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex using density functional theory. The experimentally proposed catalytic cycle is validated, in which the first step is the deprotonation of nitromethane by the ethyl anion of the catalyst, subsequently a CC bond formation step, and then the protonation of the resulting alkoxide. Three mechanistic scenarios (differing in binding modes) have been considered for the CC bond formation step. The origin of the enantioselectivity is discussed. Our calculations supported that the S configurations are the major products, which is in agreement with the experimental observations.

Theoretical investigation of the first-shell mechanism of acetylene hydration catalyzed by a biomimetic tungsten complex.

The reaction mechanism of the hydration of acetylene to acetaldehyde catalyzed by [WIVO(mnt)2]2− (where mnt2− is 1,2-dicyanoethylenedithiolate) is studied using density functional theory. Both the uncatalyzed and the catalyzed reaction are considered to find out the origin of the catalysis. Three different models are investigated, in which an aquo, a hydroxo, or an oxo coordinates to the tungsten center. A first-shell mechanism is suggested, similarly to recent calculations on tungsten-dependent acetylene hydratase. The acetylene substrate first coordinates to the tungsten center in an η2 fashion. Then, the tungsten-bound hydroxide activates a water molecule to perform a nucleophilic attack on the acetylene, resulting in the formation of a vinyl anion and a tungsten-bound water molecule. This is followed by proton transfer from the tungsten-bound water molecule to the newly formed vinyl anion intermediate. Tungsten is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Three other mechanisms are also considered, but the associated energetic barriers were found to be very high, ruling out those possibilities.

Selectivity of the α and β bond fissions for bromoacetyl chloride upon n→π* excitation: A combined complete-active-space self-consistent field and multireference configuration interaction study

The potential energy surfaces for the BrCH2COCl dissociations into Br+CH2COCl, BrCH2CO+Cl, and BrCH2+COCl in the S0, S1, and T1 states have been investigated at the complete-active-space self-consistent field, density functional theory, and multireference configuration interaction levels with the 6-31G* and cc-pVDZ basis sets, which provide some new insights into the mechanism of the BrCH2COCl photodissociation at 248 nm. It is found that the most probable pathway is the S1 C–Cl α and C–Br β bond fissions, which are a pair of competitive dissociation channels with some preference of the α C–Cl bond cleavage. The C–C α bond fission can take place along the S1 pathway upon photoexcitation at 248 nm, but it is not in competition with the C–Cl α bond cleavage. These results are consistent with the experimental findings. The relative strength of the C–C and C–Cl α bonds is one of the factors that influences the selectivity of the α bond fissions. However, the selectivity is mainly determined by the mechanism o...

Ab initio studies of dissociation pathways on the ground- and excited-state potential energy surfaces for HFCO

Potential energy surfaces of the HFCO dissociation to H+FCO and F+HCO in the lowest three electronic states (S0, S1, and T1) have been investigated with ab initio molecular orbital method at the level of the complete active space self-consistent field. An insight into the dynamics of the HFCO photodissociation at the range of 193–248 nm was provided in the present work. Radiationless transfer from S1 to T1 and subsequent dissociation on the T1 surface was predicted to be the mechanism for the C–H bond cleavage, which is consistent with that proposed by experimentalists. The experimental investigations of the HFCO photodissociation suggest that the F–C bond fission also occurs as a result of intersystem crossing (ISC) from S1 to T1, which is not supported by the present calculations. This has been discussed in detail.

An ab initio study of potential energy surfaces of CH3COCN dissociation on the low-lying states

Abstract The C–CH3 and C–CN bond dissociations of CH3COCN on S1 and T1 surfaces are studied at the CAS(8,7)/cc-pVDZ level. The results show that the intersystem crossing from S1 to T1 is a favorable pathway of S1 deactivation. Once on the T1 surface, the system can dissociate adiabatically to CH 3 ( X )+ OCCN ( X ) or CN ( X )+ CH 3 CO ( X ) , but the former has some preference over the latter. This mechanism is consistent with Chengs presumption deduced from the experimental facts and theoretical considerations. A comparison with other asymmetrically substituted carbonyl compounds suggests that the selectivity of the α-bond cleavage is mainly dependent on the mechanism of dissociation.