Journal of Theoretical and Computational Chemistry

The G3MP2B3 and P3 methods have been used to calculate the adiabatic and vertical ionization potentials (IPs) of the eight most stable tautomers of guanine. The calculated energy discrepancy between adiabatic and vertical IPs are in good agreement with the changes in geometry from neutral ground state to stable cation radicals. The geometries of imino-oxo form tautomers have no obvious change in the ionization process, which results in less energy discrepancy between vertical and adiabatic IPs. In the ionization process, the geometries of the amino-oxo and amino-hydroxy form tautomers change from nonplanar to planar structures. Hence the amino-oxo and amino-hydroxy form tautomers have larger energy discrepancy between vertical and adiabatic IPs. Further studies on the interconversion of the cation radicals shed further light on the transition process between the cation radicals and the main pathways are the hydrogen migrations and internal rotations of hydroxy (OH) and imino (NH) groups. The barriers of hydrogen rotations are lower than those of hydrogen migrations. Furthermore, the barriers for the hydrogen migrations between two rings are higher, which are about 3.0 eV.

Fluorescent proteins are important reporter molecules widely used in biotechnology and the biological sciences, generally. Their unusual spectrophotometric and fluorescence characteristics are controlled via protonation states of the chromophore, as for green fluorescent proteins (GFPs), and/or via cis–trans isomerization of the chromophore, as for red fluorescent proteins (RFPs). Here, we have performed both quantum mechanical calculations on substituted chromophores and structural comparisons of several RFPs (Rtms5, eqFP611, HcRed, and DsRed) and wild-type GFP. Our results indicate that the chromophore cis and trans isomers are comparably stable, and cis–trans isomerization has only a minor effect on electronic excitation. The chromophore is also found to exist in either the anionic or possibly zwitterionic protonation state. Structural comparisons of RFPs reveal that the conformation of the chromophore within a specific RFP is determined by only a few key residues, which could serve as mutation targets for engineering new fluorescent proteins for novel biotechnological applications.

The vector correlations between products and reactants for the reactive noncharge transfer ion–molecule collisions D⁺ + H₂ (ν=0, j = 0)→ HD + H⁺ have been determined by means of the quasiclassical trajectory method on the ground state in the KBNN potential energy surface (J Chem Phys116:654, 2002) at collision energies of 0.224, 0.524, 0.824, and 1.024 eV. The calculated differential cross section (DCS) results indicate that the lifetime of the complex in the deep well on the ground PES becomes shorter as collision energy increases. The existence of long-lived complex leads to a weak product rotational polarization at a low collision energy of 0.224 eV. However, the product rotational angular momentum j′ aligns and orients preferentially along the positive direction of the y-axis at a high collision energy of 1.024 eV. The distribution of P(θ_r, ϕ_r) indicates that the product molecules are preferentially polarized perpendicular to the scattering plane and that the reaction is dominated by an in-plane mechanism.

The insertion of singlet ¹CH₂, ¹CHF, and ¹CF₂ into polar N–H bonds of RNH₂ (R = –CH₃, –C₂H₅, –C₃H₇ or –CH(CH₃)₂) has been investigated at HF, MP2, and DFT levels using 6-31g (d, p) basis set. The insertions proceed via a two-step mechanism. The potential energy surface exploration identifies an ylide formation followed by the 1,2-proton shift concertedly giving the secondary amine. The barrier height varies with the type of carbene and amine. HOMO of amines and LUMO of carbenes control the initial interactions and it is confirmed by NBO charge analysis.

We present the theoretical DFT/B3LYP investigations on the cluster nucleation process and moving mechanism for the Pt_n (n = 1, 2, 3, 4, 8, and 12) clusters deposited on MgO surface with an embedded cluster model. The structures and energies of the Pt_n clusters adsorbed on the perfect and oxygen vacancy MgO surfaces have been calculated. Based on the nucleation of the Pt_n clusters on the oxygen vacancy sites of MgO surfaces, the two moving mechanisms of slide and rolling out of the vacancy region have been energetically investigated. The results show that the needed energies per atom moving out of the vacancy region decrease as the cluster sizes increase. Consequently, the big clusters move likely out of the vacancy sites by either slide or rolling model under a certain temperature condition.

As a typical oscillating chemical system, the frequency characteristic of photochemical oscillatory system is analyzed by a reliable oscillation frequency spectrum (OFS) approach. The results show that every periodic signal have a special OFS. The relative standard deviation (RSD) values of frequencies of four relative oscillating signals which belong to photochemical oscillatory system are extracted. They have multi-frequency characteristic. OFS successfully realizes the extraction and calculation of photochemical oscillatory system. OFS can be used to analyze the frequency of complex periodic signal accurately and be suitable for many areas.

The stereodynamics of the title reaction on the ground 1 ¹A′ potential energy surface (PES) has been studied using quasi-classical trajectory (QCT) method. Collision energy of 6.4 kcal/mol is considered, and vector properties including angular momentum alignment distributions and polarization-dependent differential cross-sections (PDDCS) of the product OH are presented. Furthermore, the influence of reagent rotational excitation and vibrational excitation on the product vector properties has also been studied in the present work. The results indicate that the distribution of the P(θ_r) and P(ϕ_r) are sensitively affected by the rotational and vibrational excitation. The rotational excitation decreases the degree of alignment and orientation, while vibrational excitation increases the degree of alignment and orientation. The PDDCS (2π/σ)(dσ₂₀/dω_t) and (2π/σ)(dσ₂₂₊/dω_t) are sensitively influenced by rotational and vibrational excitations, while the PDDCS ((2π/σ)(dσ₀₀/dω_t)) and (2π/σ)(dσ_21-/dω_t) are not. The preference of forward scattering has been found from the results of PDDCS ((2π/σ)(dσ₀₀/dω_t)), which is in good agreement with the experimental results.

Computations were carried out employing the restricted Hartree–Fock (RHF) and density functional theory (DFT) methods to investigate the geometries and energies for the 1,3-dithiole-2-thione (DTT), 1,3-dithiole-2-one (DTO), 1,3-dioxole-2-thione (DOT), and 1,3-dioxole-2-one (DOO) molecules and their radical cations. The geometrical parameters of all the four molecules suggest a finite extent of extended conjugation across the molecules. The radical cations of the DTT and DOT molecules exhibit increased extent of conjugation compared to their neutral analogues. However, on going from the neutral DOO and DTO molecules to their radical cations, the extent of conjugation across the ions decreases and two unsaturated sites become isolated from each other. Requirement of the relaxation energy for the formation of radical cation is much lower for the DTT and DOT molecules compared to that for the DOO and DTO molecules. Smaller relaxation energy requirement favors minimal resistance to charge transport along the molecular stacking. Therefore, it is speculated that the DTT and DOT molecules are better molecular conductors as compared to the DOO and DTO molecules.

The above threshold dissociation (ATD) of the HD⁺ molecular ion in a linearly polarized femtosecond laser field is theoretically studied using three-dimensional time-dependent quantum wave packet method. Based on the Born–Oppenheimer approximation (BOA), calculations are performed on two electronic states, the ground state 1sσ and the excited state 2pσ. The energy-dependent distributions of the dissociated fragments, resulting from the ATD, are calculated by using an asymptotic-flow expression in the momentum space. The numerical results demonstrate that, in the laser field of wavelength λ = 800 nm and full-width at half-maximum (FWHM) τ = 30 fs, only two-photon dissociation is observable at a weaker pulse peak intensity, 5.0 × 10¹²W cm^-2, while at an intense intensity, 1.5 × 10¹⁵W cm^-2, the dissociated fragments resulting from four-photon absorption dominates over the photodissociation process. These results are consistent with the experimental observation of Orr et al. [Orr PA et al., Phys Rev Lett98:163001, 2007]. The ac Stark-shift caused by intense laser field will change the kinetic energies of the fragments. The ATD phenomena are quantitatively interpreted in terms of the concept of light-induced potential. The molecular rotation and alignment have some effects on the kinetic energy spectrum of the dissociated fragments. The molecular rotation reduces the ac Stark-shift and broadens the peaks of kinetic energy spectra of the dissociated fragments. However, the intense laser field can effectively align the molecule and is helpful to increase the ATD probability. The ATD spectrum is related to the initial quantum numbers J₀ and M₀ of the molecule. The ATD spectrum of HD⁺ is calculated at a limited thermal temperature.

Intramolecular amide hydrolysis of N-methylmaleamic acid is revisited at the B3LYP/6-311G(2df, p)//B3LYP/6-31G(d, p) + ZVPE level, including solvent effects at the CPCM-B3LYP/6-311G(2df, p)//Onsager-B3LYP/6-31G(d, p) + ZPVE level. The concerted reaction mechanism is energetically favorable over stepwise reaction mechanisms in both the gas phase and solution. The calculated reaction barriers are significantly lower in solution than in the gas phase. In addition, it is concluded that the substituents of the four N-methylmaleamic acid derivatives considered herein have a significant effect on the gas-phase reaction barriers but a smaller, or little, effect on the barriers in solution.

The nine-dimension quasi-classical trajectory (QCT) calculations have been carried out for the title reaction with a global potential energy surface (PES) constructed by Corchado and Espinosa-García (J Chem Phys106:4013, 1997). The detailed dynamics calculations cover the specific collision energies falling in the range of 0.62–3.04 eV, which are sufficient to fit the calculated reactive cross-sections into a barrier-type excitation function and to obtain the thermal rate constants. The present QCT rate constants are in good agreement with the recent quantum dynamics (QD) results, both of which are much lower than that of the previous variational transition state theory (VTST).

In the context of quantitative structure–activity relationship (QSAR) studies the traditional statistical indices, i.e. simple correlation factor, standard error of estimates, as well as t-Student and Fisher's tests are challenged against the algebraic spectral description of the multi-linear models. While the new correlation approach is built on the algebraic (Euclidian) norms and on the associate correlation factor, the validation and predictive features are assured throughout so-called "ergodic" least action principle across the investigated models. The reliability of the present proposed spectral respecting statistical QSAR analysis is evaluated on modeling the aliphatic amines' ecotoxicity by means of hydrophobicity, polarizability, and total energy structural parameters resulting in better prediction of molecular hierarchy of observed bioactivity being susceptible to such general behavior.

This work is an attempt to evaluate theoretically the influences of oxidation and cationization on the N-glycosidic bond stability and the proton and sodium affinities on 8-oxo-2′-deoxyadenosine (8-oxodA) by using the density functional theory (DFT) B3LYP with basis set 6-31++G(d,p). This work shows that the cation attachment to 8-oxodA may modify the equilibrium geometry and bond dissociation. In all modified forms, the length of the N9–C1′ bond in which there is no intramolecular interaction, i.e. O8–H(Na)⋯O4′, increases relative to the neutral system 8-oxodA but that of others decreases. The analysis for the proton and sodium affinity energies indicates that the N1 and N3 atoms are the favorable sites for proton while the N1 atom is the favorable site for Na⁺. From the dissociation energies of the N-glycosidic bond, it has been found that the homolytic dissociation becomes more difficult upon introducing positive charge in the base ring. In contrast, these systems favor the heterolytic dissociation significantly. The influence is most prominent with the monocation obtained by O8 cationization.

HIV-1 protease (PR) is a primary target for anti-HIV therapeutics. A well conserved water molecule, denoted as W301, is found in almost all the crystallographic structures of PR/inhibitor complexes and it plays an important role in PR/inhibitor binding. As the PR/inhibitor interaction depends on the ionization state of the cleavage site which contains an aspartyl dyad (Asp25/Asp25′), the determination of the protonation states of aspartyl dyad in PR may be essential for drug design. In this study, a linear scaling quantum mechanical method, molecular fragmentation with conjugate caps (MFCC), is used for interaction study of PR/ABT-538 and W301 at four different monoprotonation states of the Asp25/Asp25′. Combined method of MFCC and conductor-like polarizable continuum model (CPCM) is applied in binding affinity calculation for four minimum energy structures which are extracted from four different molecular dynamics trajectories corresponding to four different monoprotonation states of Asp25/Asp25′. Our result is in good agreement with previous result obtained by FEP/TI method, showing that the conserved W301 contributes significantly to the binding free energy of PR/ABT-538 complex and different protonation states of Asp25/Asp25′ have significant impact on the binding free energy contribution from W301.

Protein tyrosine phosphatase 1B (PTP1B) is one of the important regulators of signal transduction pathways. The present study aims to investigate the effect of Arg 221 on the active site of PTP1B. Six mutants were carried out using Schrödinger Suite 2007 and molecular dynamics simulation was performed by using the Tinker package. Results show that point mutations at position 221 have great influence on shape of active site, backbone movement of active site, and interaction between substrate and PTP1B. R221H and R221K lead to increased total interaction energies. R221G, R221F and R221T cause increase in total interaction energies, but decrease in interaction energies between pTyr 4 and P loop (catalytic residues). R221E results in both decreased total interaction energies and interaction energies between pTyr 4 and P loop. This indicates that Arg 221 mutated to basic residues can lead to enhanced binding affinity between substrate and protein; when mutated to acidic residues it will decrease binding affinity and catalytic activity; other kinds of mutations result in increased binding affinity but decreased catalytic activity.

Electron transfer dynamics in donor–bridge–acceptor (DBA) systems under dissipative environment is investigated by using the quasi-adiabatic propagator path integral approach. The dephasing and relaxation rates are extracted from the Fourier transform of the time-dependent population difference of the donor and the acceptor states. Comparing the rates obtained from the DBA and the effective two state systems, respectively, we reveal the validity of the superexchange mechanism. It is found that the coupling of the environment to the bridges does not affect the superexchange rates for the bridges having high enough electronic energies, and the superexchange mechanism still works quite well even though the population on the bridges is over than 0.2 in a tested system.