Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study

Aromatic ring-peptide bond interactions (modeled as benzene and formamide, N-methylformamide and N-methylacetamide) are studied by means of advanced computational chemistry methods: second-order M?ller-Plesset (MP2), coupled-cluster single and double excitation model [CCSD(T)], and density functional theory with dispersion (DFT-D). The geometrical preferences of these interactions as well as their interaction energy content, in both parallel and T-shaped arrangements, are investigated. The stabilization energy reaches a value of over 5 kcal/mol for the N-methylformamide-benzene complex at the CCSD(T)/complete basis set (CBS) level. Decomposition of interaction energy by the DFT-symmetry-adapted perturbation treatment (SAPT) technique shows that the parallel and T-shaped arrangements, although similar in their total interaction energies, differ significantly in the proportion of electrostatic and dispersion terms.     

烷基锂分子中化学键的 ab initio 研究

本文用6-13G基函对3-12G基优化构型进行单点ab initio (从头计算法) 计算, 并根据轨道的组合系数、电荷密度图和键强参数等详尽地分析了烷基锂分子的成键情况。烷基锂的易挥发、易聚合、聚合物易溶于烃类溶剂中等物理、化学性质主要是其C－Li键具有显著的共价性缘故。由于烷基锂的C-Li键比C－H和C－C键的强度要小,故C-Li键易于断裂,使烷基锂表现有高的化学反应活性。     

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

Solvent effect on conical intersections in excited-state 9H-adenine: radiationless decay mechanism in polar solvent

The ground- and excited-state free energy minima and the conical intersections among these states of 9H-adenine in aqueous and acetonitrile solutions are studied theoretically to elucidate the mechanism of radiationless decay. We employ the recently proposed linear-response free energy (LRFE) to locate the energy minima and conical intersections in solution. The LRFE is calculated by using the reference interaction site model self-consistent field method. The geometry optimizations are carried out at the complete active space self-consistent field level, and the dynamic electron correlation energies are estimated by the multireference M?ller-Plesset method. We find that the conical intersection between the (1)L(a) and (1)L(b) states in aqueous solution occurs at a wide area of the free energy surface, indicating a strong vibronic coupling between them. On the other hand, the (1)npi(*) state is largely blue-shifted at planar geometries in solution, which suggests that the nonadiabatic transition to this state is suppressed. The importance of the (1)pisigma(*) channel is also examined in both the gas phase and solution. Based on the free energy characteristics obtained by the calculations, we intend to explain the experimental observations that the excited state of 9H-adenine decays monoexponentially with shorter lifetimes in polar solvents than that in the gas phase.     

Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations

The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic simulations combined with high-level correlated ab initio quantum chemical and statistical thermodynamic calculations. The lowest energy conformers were localized in the free energy surface. The structures of the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas phase have been for the first time reported and their scaled theoretical IR spectra unambiguously assigned and compared with previous gas-phase experimental results. Common geometrical features have been systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly. In addition, the peptide backbone of Trp-Gly-Gly has been compared with that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur. J. 2005, 11, 6803). From the observed systematic structural behavior between these peptide analogues, it is expected that the gas-phase conformers of other similar aromatic small peptides would present equivalent geometries. The DFT methodology failed to describe the potential energy surface of the studied peptides since the London dispersion energy (not covered in DFT) plays a significant role in the stabilization of most stable conformers.     

An ab initio study of the CH3I photodissociation. II. Transition moments and vibrational state control of the I* quantum yields

Multireference spin-orbit configuration interaction calculations of transition moments from the X A1 ground state to the 3Q0+, 3Q1, and 1Q excited states responsible for the A absorption band of CH3I are reported and employed for an analysis of the photofragmentation in this system. Contrary to what is usually assumed, the 3Q0+(A1), 3Q1(E), and 1Q(E)<--X A1 transition moments are found to be strongly dependent on the C-I fragmentation coordinate. The sign of this dependence is opposite for the parallel and perpendicular transitions, which opens an opportunity for vibrational state control of the photodissociation product yields. The computed absorption intensity distribution and the I* quantum yield as a function of excitation energy are analyzed in comparison with existing experimental data, and good agreement between theory and experiment is found. It is predicted that significantly higher I* quantum yield values (>0.9) may be achieved when vibrationally hot CH3I molecules are excited in the appropriate spectral range. It is shown that vibrational state control of the I*/I branching ratio in the alkyl (hydrogen) iodide photodissociation has an electronic rather than a dynamic nature: Due to a different electron density distribution at various molecular geometries, one achieves a more efficient excitation of a particular fragmentation channel rather than influences the dynamics of the decay process.     

Experimental and ab initio study of a new D 1Deltag state of the C3 radical

We report here the first observation of the D (1)Delta(g) state of the C(3) radical, which provides the first comprehensively analyzed example of the dynamic Renner-Teller splitting in Delta symmetry. Two color double resonance spectroscopy via the A (1)Pi(u) state was employed to experimentally probe an extensive range of vibronic levels in this D (1)Delta(g) state, covering all three modes of vibration of C(3). The analysis was supported by ab initio potential energy surface calculations on the C(3) radical to outline the lowest eight singlet electronic states. Two methods were used to analyze the Renner-Teller effect. The first method is an empirical Hamiltonian based on normal modes, using harmonic oscillator functions as a basis, with Renner-Teller and other terms added as required, which allows conventional vibrational parameters to be determined. The second is a much larger program that uses the exact kinetic energy operator for a triatomic molecule to calculate vibronic energy levels directly from the Renner-Teller pair of potential energy surfaces. Both methods give a good fit to the experimental results, with only a small adjustment to the ab initio surfaces required for the latter. One of the overall conclusions is that the Renner-Teller effect is rather smaller in the D (1)Delta(g) state than in the A (1)Pi(u) state.     

Diketoacid HIV-1 integrase inhibitors: An ab initio study

The stable tautomeric forms of two representative arene-substituted diketoacid HIV-1 integrase inhibitors, 5-ClTEP and L-731,988, were investigated by B3LYP with 6-31G*, 6-31G(d,p), and 6-31+G(d,p) basis sets. Optimization with MP2/6-31G* was also performed for 5-ClTEP. The solvation effect was considered using a conductor-like screening model. With the density functional theory method, the trans diketo conformations are more stable than the cis conformers. The difference is 14 kJ mol(-1) for 5-ClTEP and 33 kJ mol(-1) for L-731,988. Two trans diketo structures were obtained. The difference between these two trans diketo structures is less than 4 kJ mol(-1) calculated at the B3LYP/6-311+G(3df,2p) level. Two enol forms prevail over the diketo tautomers and are calculated to have the same free energy. Because there is no barrier observed between these two enol forms, they can interchange easily such that a delocalized transition state is suggested to be the observed form. Contradictory to the results of the MP2 method that predicts a preference for the trans diketo forms, the B3LYP method predicts a preference for the enol tautomers, which is in agreement with the experimental results.     

Investigation of structure of liquid 2,2,2 trifluoroethanol: neutron diffraction, molecular dynamics, and ab initio quantum chemical study

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the "Monte Carlo determination of g(r)" (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.     

Effect of chemical substituents on the energetical landscape of a molecular photoswitch: an ab initio study

The effect of chemical substitutions on the energetical landscape of an optical molecular switch (Phys. Chem. Chem. Phys. 2008, 10, 1243) was studied with the aid of ab initio electronic structure methods. Series of different chemical moieties were substituted into the molecular frame of 7-hydroxyquinoline as well as into the "molecular crane" at position 8 of the frame. It was shown that the π-electron-donating/withdrawing properties of substituents substantially modify the energetical landscape of the system in the ground as well as in the lowest excited ππ* and nπ* singlet states.     

Electronic structure and anisotropic chemical bonding in TiNF from ab initio study

Accounting for disorder in anatase titanium nitride fluoride TiNF is done through atoms re-distributions based on geometry optimizations using ultra soft pseudo potentials within density functional theory DFT. The fully geometry relaxed structures are found to keep the body centering of anatase (I4₁/amd No. 141). The new structural setups are identified with space groups I-4m2 No. 119 and Imm2 No. 44 which obey the “group to subgroup” relationships with respect to anatase. In the ground state Imm2 structure identified from energy differences, TiNF is found semi-conducting with similar density of states features to anatase TiO₂ and a chemical bonding differentiated between covalent like Ti-N versus ionic like Ti-F. Inter-anion N-F bonding is also identified.     

Energy bands and bond alternation potential in poly(para-phenylene vinylene): a comparative ab initio quantum chemical and density functional theory study

We present calculations of the total energy per unit cell for different bond alternations of the C-C bonds bridging the distance between two aromatic rings in poly(para-phenylene vinylene) (PPV), using two different parametrizations of the energy functional in the local density approximation (LDA) and the ab initio Hartree-Fock (HF) method. For the application of correlation corrections to the HF results the system is already too large. We find that even simple LDA methods are reliable alternatives to the ab initio HF method for the calculation of potential surfaces in polymers with large unit cells. The results in turn can be used to determine parameters for model Hamiltonians necessary for theoretical studies of the dynamics of nonlinear quasiparticles in the polymers. We further present the LDA band structures of PPV together with their HF and correlation (many body perturbation theory of 2^nd order in Møller-Plesset partitioning, MP2) corrected counterparts. We find that the fundamental gap obtained is too large both with HF and with the correlation corrected band structure compared to experiment. However, we use only a modest correlation method and a small basis set, which already brings us to the limits of the computers available to us. The LDA gaps on the other hand are too small which, however, could be corrected with the help of self interaction corrections. None of the latter methods would lead to exceedingly large computation times.     

An ab initio quantum chemical study of the electronic structure and stability of the pyrrolyl radical: Comparison with the isoelectronic cyclopentadienyl radical

The electronic structure and stability of pyrrolyl are investigated using CASSCF, CASPT2 and G2(MP2) techniques. The ground state of pyrrolyl is found to be ²A₂, with five π-electrons, as in cyclopentadienyl. The computed N–H bond energy of pyrrole is 94.8 kcal mol⁻¹, while the heat of formation Δ_fH₂₉₈^o of pyrrolyl is deduced to be 70.5±1 kcal mol⁻¹. The Arrhenius parameters of N–H and C–H bond fission in pyrrole and cyclopentadiene and hydrogen abstraction reactions (by hydrogen) were also computed, indicating that pyrrolyl forms predominantly by C–H bond fission of pyrrolenine rather than by direct N–H bond fission.     

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.     

Hydrolysis of cyclic phosphates by ribonuclease A: a computational study using a simplified ab initio quantum model

The second step in the enzyme-catalyzed hydrolysis of phosphate esters by ribonuclease A (RNase A) was studied using an ab initio quantum-based model of the active site including constrained parts of three critical residues, His-12, His-119, and Lys-41, and a small substrate. The competition between release of the cyclic phosphate intermediate and subsequent hydrolysis following transphosphorylation was explored to determine the electronic factors that contribute to preferential intermediate product release observed experimentally. The structural and energetic results obtained at both the RHF and MP2 levels reveal several contributing factors consistent with experimental observation. Although the intrinsic electronic effects tend to favor hydrolysis slightly with an overall activation free energy of approximately 70 kJ mol(-1), entropic and environmental effects favor release of the cyclic phosphate intermediate over hydrolysis. Exploration of the second, hydrolysis step also revealed interesting similarity with the transphosphorylation step, including the observation of autocatalysis by the substrate. Moreover, both steps of the overall RNase A reaction reveal multiple pathways involving proton transfers to sites of similar proton affinities. The anionic phosphate in both steps can act as a stable proton binding site as protons are moved around the active site throughout the progress of the reaction. These results suggest autocatalysis may be representative of more general behavior in enzymes containing highly charged substrates, especially phosphates.     

Distinguishing between relaxation pathways by combining dissociative ionization pump probe spectroscopy and ab initio calculations: a case study of cytosine

We present a general method for tracking molecular relaxation along different pathways from an excited state down to the ground state. We follow the excited state dynamics of cytosine pumped near the S(0)-S(1) resonance using ultrafast laser pulses in the deep ultraviolet and probed with strong field near infrared pulses which ionize and dissociate the molecules. The fragment ions are detected via time of flight mass spectroscopy as a function of pump probe delay and probe pulse intensity. Our measurements reveal that different molecular fragments show different timescales, indicating that there are multiple relaxation pathways down to the ground state. We interpret our measurements with the help of ab initio electronic structure calculations of both the neutral molecule and the molecular cation for different conformations en route to relaxation back down to the ground state. Our measurements and calculations show passage through two seams of conical intersections between ground and excited states and demonstrate the ability of dissociative ionization pump probe measurements in conjunction with ab initio electronic structure calculations to track molecular relaxation through multiple pathways.     

An ab initio study of the excited States, isomerization energy profiles and conical intersections of a chiral cyclohexylidene derivative

The excited valence and Rydberg states of the chiral (4-methylcyclohexylidene) fluoromethane (4MCF) have been investigated using multiconfigurational CASSCF and CASPT2, and coupled-cluster methods (RI-CC2). A 3s Rydberg state is predicted below the valence (1)pipi* state. To gain insight into the photophysics of the cis-trans isomerization of this olefin, potential energy profiles for the valence (10pipi* state along the twisting and pyramidalization reaction coordinates have been computed using variational methods (CASSCF and multireference configuration interaction with singles and doubles (MR-CISD)). Starting from geometries with energies close to degeneracy in the valence and ground-state curves, three minima on the crossing seam that can be correlated with the conical intersections known for fluoroethylene, have been found. On the basis of these features, the photochemistry of 4MCF is discussed.     

YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model

A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.     

The 1:1 glycine zwitterion-water complex: An ab initio electronic structure study

More than a dozen stationary points on the potential energy surface for the 1:1 glycine zwitterion—water complex have been investigated at Hartree-Fock or MP2 levels of theory with basis sets ranging from split valence (4-31G) to split valence plus polarization and diffuse function (6–31 + + G**) quality. Only one true minimum (GLYZWM, C₁ symmetry) could be located on the potential energy surface. GLYZWM features a bridged water molecule acting as both a hydrogen bond acceptor and donor with the NH₃⁻ and CO₂⁻ units of the glycine zwitterion. The total hydrogen bond energy in GLYZWM is computed as 16 kcal/mol (MP2/6–31 ++ G** // 6–31 ++ G**, including corrections for basis set superpositions errors). The computed vibrational frequencies and normal mode forms of the GLYZWM complex resemble in many cases experimental assignments made for the glycine zwitterion in bulk water on the basis of Raman spectroscopy. © 1996 by John Wiley & Sons, Inc.