The thermal stability and thermal activity of four G90D rhodopsin isomer models were investigated by QM/MM method. The results implied that one pathological mechanism of congenital stationary night blindness caused by G90D mutation is the low thermal isomerization barrier of G90D rhodopsin binding with 11-cis retinal, not just the lacking of natural salt bridge. 9-cis retinal binding with G90D rhodopsin opsin could increase the thermal stability and minimize the thermal isomerization of G90D rhodopsin mutant. Therefore, 9-cis retinal was suggested to be used in potential treatments for congenital stationary night blindness caused by G90D mutation.

•The absorption spectral tuning mechanism of E113Q rhodopsin in dark state at different pH values is elaborated.•The counterions around Schiff base are more crucial than the protein environments to affect the absorption spectra of E113Q.•E113Q rhodopsin has the potential for use as a template of anion biosensors at visible wavelength.The absorption spectra of bovine rhodopsin mutant E113Q in solutions were investigated at the molecular level by using a hybrid quantum mechanics/molecular mechanics (QM/MM) method. The calculations suggest the mechanism of the absorption variations of E113Q at different pH values. The results indicate that the polarizations of the counterions in the vicinity of Schiff base under protonation and unprotonation states of the mutant E113Q would be a crucial factor to change the energy gap of the retinal to tune the absorption spectra. Glu-181 residue, which is close to the chromophore, cannot serve as the counterion of the protonated Schiff base of E113Q in dark state. Moreover, the results of the absorption maximum in mutant E113Q with the various anions (Cl−, Br−, I− and NO3−) manifested that the mutant E113Q could have the potential for use as a template of anion biosensors at visible wavelength.

We present here a double-optimizations-of-buffer-region (DOBR) microiterative scheme for high-efficiency energy minimizations of large, flexible systems in combined quantum-mechanical/molecular-mechanical (QM/MM) calculations. In the DOBR scheme, an entire system is divided into three regions: the core, buffer, and outer regions. The core region includes QM atoms and the MM atoms within a cutoff distance R1 to the QM atoms (denoted by MM1 atoms), and the buffer region consists of MM atoms within another cutoff distance R2 to MM1 atoms. Each DOBR microcycle involves two steps: First, QM atoms are assigned electrostatic-potential (ESP) charges, and the buffer and outer regions are optimized at the MM level with the core region kept frozen. Second, the core and buffer regions are optimized at the QM/MM level using the electrostatic embedding with the outer region kept frozen. The two steps are repeated until two optimizations converge at one structure. The DOBR scheme was tested in the optimizations of nucleobases solvated in water spheres of 30 Å radius, where the initial geometries were extracted from the trajectories of classical molecular dynamics simulations, and the cutoff distances R1 and R2 were set to 5.0 and 4.0 Å, respectively. For comparisons, the optimizations were also carried out by a “standard” scheme without microiteration and by the two-region microiterative (TRM) method. We found that the averaged number of QM calculations for the DOBR scheme is only ∼1% of that of the standard scheme and ∼6% of the TRM approach. The promising results indicate that the DOBR scheme could significantly increase the efficiency of geometry optimizations for large, flexible systems in QM/MM calculations.

•The collision time is affected by the collision energy and initial vibrational level.•The effect of the collision time on some product distributions is calculated.•The majority of the reactivity is focused on several concentrated regions.•There is a “competition” among different parts of the reactivity.•Two types of trajectories in accordance with two mechanisms are identified.The collision time which describes the speed of the collision process in a reaction is an important concept to an elementary chemical reaction. In this study, the quasiclassical trajectory method is applied to investigate the collision time of the reaction Ca + HCl (v = 0–2, j = 0) → CaCl + H. In order to provide a clear image of the reaction, the integral cross section we calculated is compared with corresponding quantum result and shows fairly good agreement. The results indicate that the collision energy and the initial vibrational level affect the average collision time remarkably. As the collision energy or the initial vibrational level increases, the average collision time decreases. The difference of average collision time for different initial vibrational level decreases with the increasing of collision energy. The product distributions as functions of scattering angle, attack angle and impact parameter are computed. Observing the functions, it can be found that the features could be caused by a competition among different parts of the product molecules with different collision time. For all the investigated initial vibrational levels, most of the reactive trajectories have the shorter collision times and are focused in several concentrated regions. Two possible mechanisms could be responsible for the HCl (v = 0) reaction in the concentrated regions. One is the sideway scattering and the system would fall into the deep potential well once in the collision process. The other is the weak forward scattering and strong backward scattering. The system would go around the deep potential well in the collision process. It is shown that the character of the weak forward scattering and strong backward scattering for the HCl (v = 1 and 2) reactions in the concentrated regions. However, the reactions outside the concentrated regions have the longer collision times and no particular mechanism. In the collision process, the system could fall into the deep potential well many times. We also explored the dynamics of the reaction at the same total energies but for different initial vibrational levels and found that the role of the insertion well becomes less and less important with the increasing of total energy.The collision time is affected by the collision energy and initial vibrational level remarkably. The majority of the reactivity could be explained by two mechanisms.

State-to-state quantum dynamics calculations for the H + LiH (v = 0–1, j = 0) → H2 + Li reactions are performed based on an ab initio ground electronic state potential energy surface (PES). Total and product state-resolved integral and differential cross sections and rate constants are calculated. The present total integral cross sections and rate constants for the H + LiH (v = 0, j = 0) reaction are found to be in agreement with previous literature results. Product state-resolved integral cross sections and rate constants reveal that the H2 products are preferred to be formed in their rovibrational excited states. The differential cross sections show that the intensity of forward scattering for the H2 products in their rovibrational excited states is stronger than other states. The mechanisms for the v = 0 and v = 1 reactions are found to be highly consistent with each other. Further, the influence of the stripping mechanism on the H + LiH reaction is studied. It is found that the stripping mechanism could be responsible for the decrease of the reactivity, the product state distribution, and scattering direction of the H2 products. It is related to the “attractive” feature of the underlying PES.

•Geometric structures of clusters 4AP-(H2O)n (n = 1–7) in states S0 and S1 were optimized.•In S1 state, A-type hydrogen bond is weakened whereas B- and C-type hydrogen bonds are strengthened.•Weakening of A causes blueshifts of absorption and infrared spectra.•Strengthening of B and C leads to redshifts of electronic and infrared spectra.TD-DFT and DFT calculations have been performed to examine the relationship between the spectral shifts of 4-aminophthalimide (4AP) and the formation of hydrogen bonds in water solution. The computations of the S0 state are at the IEFPCM-B3LYP/6-311++G(d, p) level and the S1 state at the TD-IEFPCM-B3LYP/6-311++G(d, p) level. The eleven structures of the hydrogen-bonded 4AP clusters formed with different number water molecules in both S0 and S1 states were optimized. The absorption, fluorescence and infrared spectra were calculated. The results of the hydrogen bond energy and length reveals that the hydrogen bonds formed by the nitrogen atom of the amine group with water molecule (A type) are significantly weakened from states S0 to S1. In contrast, the hydrogen bonds formed by the oxygen atoms of the two carbonyl groups (B type) with water molecules and those formed by the two hydrogen atoms of the amine group (C type) with water molecules are remarkably strengthened. Comparing with the 4AP monomer spectra, the weakening for the hydrogen bond of A type could be responsible for the blueshifts of the electronic absorption spectra and the stretching vibrational spectra of the two NH groups in 4AP from states S0 to S1. The significant redshifts of the electronic spectra and the S0–S1 downshifts of the stretching vibrational modes of the two NH groups and the two carbonyl groups in 4AP could be attributed to the strengthening of hydrogen bonds for B and C types.Graphical abstract