Promising and efficient lignin degradation versatile strategy based on DFT calculations.

The extraction of higher-value products from lignin degradations under mild conditions is a challenge. Previous research reported efficient two-step oxidation and reduction strategies for lignin degradation, which has great significance to lignin degradation. In this paper, the mechanism about the C-O bond cleavage of lignin with and without Cα oxidations has been studied systematically.

Insight into the drug resistance mechanisms of GS-9669 caused by mutations of HCV NS5B polymerase via molecular simulation.

GS-9669 is a non-nucleos(t)ide inhibitor (NNI) binding to the thumb site II of the Hepatitis C virus (HCV) NS5B polymerase and has advanced into phase II trials. To clarify the drug resistance mechanisms of GS-9669 caused by M423T/I/V, L419M, R422K, and I482L mutations of NS5B polymerase (GT1b) and the receptor-ligand interactions during the binding process, a series of molecular simulation methods including molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed for the wild-type (WT) and six mutant NS5B/GS-9669 complexes. The calculated results indicate that the binding free energies of the mutant systems are less negative than that of the WT system, indicating that these mutations will indeed cause NS5B to produce different degrees of resistance to GS-9669.

Computational insight into the mechanisms of action and selectivity of Afraxis PAK inhibitors.

The p21-activated kinases (PAKs) are involved in many important biological activity regulations. FRAX019, FRAX414, FRAX597, FRAX1036 and G-5555 were identified as PAKs inhibitors. Their detailed inhibitory mechanisms deserve further investigation.

Molecular modeling study on the drug resistance mechanism of NS5B polymerase to TMC647055.

NS5B polymerase plays an important role in viral replication machinery. TMC647055 (TMC) is a novel and potent non-nucleoside inhibitor of the HCV NS5B polymerase. However, mutations that result in drug resistance to TMC have been reported.

Computational study on the drug resistance mechanism of HCV NS3 protease to BMS-605339.

NS3 protease plays a vital role in the replication of the hepatitis C virus (HCV). BMS-605339 is a novel linear tetra-peptide α-ketoamide inhibitor of NS3 protease and shows specificity for HCV NS3 protease genotype 1a and genotype 1b. Mutation at the key site 168 of the HCV NS3 protease can induce resistance to BMS-605339, which greatly affects the antiviral therapy efficacy to hepatitis C.

Divalent metals can reside on bonds in fullerenes.

DFT calculations consistently suggest that a lanthanide will sit on either the 6/6 bond inside C60 having a divalent state or the hexagonal center having a trivalent state. Some lanthanides can stay only above the 6/6 bond inside C60 to form stabilized structures, despite the greatly reduced metal-cage coordination numbers. The preference for C-C bonds by a divalent metal has been confirmed by revisiting the structures of Yb@C2v(3)-C80, Yb@Cs(6)-C82 and Yb@C2v(9)-C82, for which the calculations suggest that the Yb atoms are indeed situated above the C-C bonds, close to the reported structures obtained by single crystal XRD experiments.

Computational study on the drug resistance mechanism of HCV NS5B RNA-dependent RNA polymerase mutants V494I, V494A, M426A, and M423T to Filibuvir.

Filibuvir, a potent non-nucleoside inhibitor of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp), has shown great promise in phase IIb clinical trial. However, drug resistant mutations towards Filibuvir have been identified. In the present study, the drug resistance mechanism of wild-type (WT) and mutant NS5B polymerases (including V494I, V494A, M426A, and M423T) toward Filibuvir was investigated by molecular modeling methods.

Computational study on the molecular mechanisms of drug resistance of Narlaprevir due to V36M, R155K, V36M+R155K, T54A, and A156T mutations of HCV NS3/4A protease.

Narlaprevir is a novel NS3/4A protease inhibitor of hepatitis C virus (HCV), and it has been tested in a phase II clinical trial recently. However, distinct drug-resistance of Narlaprevir has been discovered. In our study, the molecular mechanisms of drug-resistance of Narlaprevir due to the mutations V36M, R155K, V36M+R155K, T54A, and A156T of NS3/4A protease have been investigated by molecular dynamics (MD) simulations, free energy calculations, and free energy decomposition analysis.

Photodissociation mechanisms of the CO2(2+) dication studied using multi-state multiconfiguration second-order perturbation theory.

Employing the multi-state multiconfiguration second-order perturbation theory (MS-CASPT2) and complete active space self-consistent field (CASSCF) methods, the geometries, relative energies (T(v)') to the ground state (X(3)Σg(-)), adiabatic excited energies, and photodissociation mechanisms and corresponding kinetic energy releases for the lower-lying 14 electronic states of the CO2 (2+) ion are studied. The T(v)' values are calculated at the experimental geometry of the ground state CO2 molecule using MS-CASPT2 method and highly close to the latest threshold photoelectrons coincidence and time-of-flight photoelectron photoelectron coincidence spectrum observations. The O-loss dissociation potential energy curves (PECs) for these 14 states are drawn using MS-CASPT2 partial optimization method at C(∞v) symmetry with one C-O bond length ranging from 1.

The Bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory.

The Bergman cyclizations of the enediyne and its four N-substituted analogs [(Z)-pent-2-en-4-ynenitrile, 3-azahex-3-en-1,5-diyne, malenotrile, and 3,4-azahex-3-en-1,5-diyne] have been studied using the complete active space self-consistent field and multiconfigurational second-order perturbation theory methods in conjunction with the atomic natural orbital basis sets. The geometries and energies of the reactants, transition states, and products along both the S(0) (the ground state) and T(1) (the lowest-lying triplet state) potential energy surfaces (PESs) were calculated. The calculated geometries are in good agreement with the available experimental data.

Low-lying electronic states and Cl-loss photodissociation of the C2H3Cl+ ion studied using multiconfiguration second-order perturbation theory.

We studied the 1(2)A' '(X2A' '), 1(2)A' (A2A'), 2(2)A' ' (B2A' '), and 2(2)A' (C2A') states of the C2H3Cl+ ion using the complete active space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) methods. For the four ionic states, we calculated the equilibrium geometries, adiabatic (T0) and vertical (Tv) excitation energies, and relative energies (Tv') at the geometry of the molecule at the CASPT2 level and the Cl-loss dissociation potential energy curves (PECs) at the CASPT2//CASSCF level. The computed oscillator strength f value for the X2A' ' <-- A2A' transition is very small, which is in line with the experimental fact that the A state has a long lifetime.

Dissociation of the OCS+ ion in low-lying electronic states studied using multiconfiguration second-order perturbation theory.

Complete active space self-consistent-field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) calculations with atomic natural orbital basis sets were performed to investigate the S-loss direct dissociation of the 1 2Pi(X 2Pi), 2 2Pi(A 2Pi), 1 2Sigma+(B 2Sigma+), 1 4Sigma-, 1 2Sigma-, and 1 2Delta states of the OCS+ ion and the predissociations of the 1 2Pi, 2 2Pi, and 1 2Sigma+ states. Our calculations indicate that the S-loss dissociation products of the OCS(+) ion in the six states are the ground-state CO molecule plus the S+ ion in different electronic states. The CASPT2//CASSCF potential energy curves were calculated for the S-loss dissociation from the six states.

Cl-loss and H-loss dissociations in low-lying electronic states of the CH3Cl+ ion studied using multiconfiguration second-order perturbation theory.

To examine the experimentally suggested scheme of the pathways for Cl- and H-loss dissociations of the CH(3)Cl(+) ion in the X(2)E (1(2)A', 1(2)A' '), A(2)A(1) (2(2)A'), and B(2)E (3(2)A', 2(2)A") states, the complete active space-self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) calculations with an atomic natural orbital (ANO) basis were performed for the 1(2)A' (X(2)A'), 1(2)A", 2(2)A', and 2(2)A'" states. The potential energy curves describing dissociation from the four C(s) states were obtained on the basis of the CASSCF partial geometry optimization calculations at fixed C-Cl or C-H distance values, followed by the CASPT2 energy calculations. The electronic states of the CH3(+) and CH(2)Cl(+) ions produced by Cl-loss and H-loss dissociation, respectively, were carefully determined.

F-loss and H-loss dissociations in low-lying electronic states of the CH3F+ ion studied using multiconfiguration second-order perturbation theory.

Complete active space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) calculations with an atomic natural orbital basis were performed for the 1(2)A'', 1(2)A', 2(2)A', 2(2)A'', and 3(2)A' (X2E, A2A1, and B2E) states of the CH3F+ ion. The 1(2)A'' state is predicted to be the ground state, and the C(s)-state energy levels are different from those of the CH3Cl+ ion. The 2(2)A' (A2A1) state is predicted to be repulsive, and the calculated adiabatic excitation energies for 2(2)A'' and 3(2)A' are very close to the experimental value for the B state.

The 1 (2)A(1), 1 (2)B(2), and 1 (2)A(2) states of the SO(2) (+) ion studied using multiconfiguration second-order perturbation theory.

The 1 (2)A(1), 1 (2)B(2), and 1 (2)A(2) electronic states of the SO(2) (+) ion have been studied using multiconfiguration second-order perturbation theory (CASPT2) and two contracted atomic natural orbital basis sets, S[6s4p3d1f]/O[5s3p2d1f] (ANO-L) and S[4s3p2d]/O[3s2p1d] (ANO-S), and the three states were considered to correspond to the observed X, B, and A states, respectively, in the previous experimental and theoretical studies. Based on the CASPT2/ANO-L adiabatic excitation energy calculations, the X, A, and B states of SO(2) (+) are assigned to 1 (2)A(1), 1 (2)B(2), and 1 (2)A(2), respectively, and our assignments of the A and B states are contrary to the previous assignments (A to (2)A(2) and B to (2)B(2)). The CASPT2/ANO-L energetic calculations also indicate that the 1 (2)A(1), 1 (2)B(2), and 1 (2)A(2) states are, respectively, the ground, first excited, and second excited states at the ground-state (1 (2)A(1)) geometry of the ion and at the geometry of the ground-state SO(2) molecule.