Molecular dynamics simulations of the Escherichia coli HPPK apo-enzyme reveal a network of conformational transitions.

6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that even when confined by crystal contacts, loops 2 and 3 remain rather flexible when the enzyme is in its apo form, raising questions about the putative large-scale induced-fit conformational change of HPPK. To investigate the loop dynamics in a crystal-free environment, we performed conventional molecular dynamics simulations of the apo-enzyme at two different temperatures (300 and 350 K). Our simulations show that the crystallographic B-factors considerably underestimate the loop dynamics; multiple conformations of loops 2 and 3, including the open, semi-open, and closed conformations that an enzyme must adopt throughout its catalytic cycle, are all accessible to the apo-enzyme. These results revise our previous view of the functional mechanism of conformational change upon MgATP binding and offer valuable structural insights into the workings of HPPK. In this paper, conformational network analysis and principal component analysis related to the loops are discussed to support the presented conclusions.

Tuning the electronic and phosphorescence properties of blue-emitting iridium(III) complexes through different cyclometalated ligand substituents: a theoretical investigation.

The geometric and electronic structures, phosphorescence properties and the organic light-emitting diode (OLED) performance of a series of Ir(III) complexes based on bis[(4,6-di-fluorophenyl)-pyridinato-N,C2']picolinate (FIrpic) were investigated by using density functional theory/time-dependent density functional theory (DFT/TD-DFT), including Ir(III)bis[2-(2,4-difluorophenyl)-4-(tert-butyl)pyridinato-N,C2']picolinate (1a), Ir(III)bis[2-(2,4-difluorophenyl)-4-(n-heptyl)pyridinato-N,C2']picolinate (2a), Ir(III)bis[2-(2,4-difluorophenyl)-4-(3-ethylheptyl)pyridinato-N,C2']picolinate (3a), Ir(III)bis[2-(2,4-difluorophenyl)-4-(2,4,6-trimethylphenyl)pyridinato-N,C2']picolinate (5a), and Ir(III)bis[2-(2,4-difluoro-3-(2,4,6-trimethylphenyl)phenyl)-pyridinato-N,C2'] picolinate (5b). To explore the influence of the substituted positions on the optical and electronic properties of the Ir(III) complexes, seven other new complexes were designed by introducing the substituted groups on the difluorophenyl rings or pyridine rings. After introducing the phenyl substituted groups on the pyridine or difluorophenyl rings of cyclometalated ligands, the HOMO-LUMO energy gap is decreased. Thus, the absorption spectra of 4a and 4b undergo a red-shifting, especially for 4a, and have a stronger absorption strength that will be beneficial to improving their quantum yields, which is proved by the further evaluation of the radiative (k(r)) and non-radiative (k(nr)) rate constants. The combinations of a larger (3)MLCT-(3)MC energy gap, smaller ΔE(S1-T1), and higher contribution of (3)MLCT in the emission process result in the higher quantum yields for complexes 4a and 4b. Besides, the designed complexes 4a and 4b are considered to be potential candidates as blue-emitting materials with better equilibrium between the hole transport (λ(hole)) and electron transport (λ(electron)).

Dual emission behavior of phenyleneethynylene gold(I) complexes dictated by intersystem crossing: a theoretical perspective.

In commonly studied gold(I) complexes with oligo (o-, p-, or m-phenyleneethynylene) (PE) ligands, an intriguing photophysical behavior is dual emission composed of fluorescence from S1 and phosphorescence from T1 which is dictated by effective intersystem crossing (ISC) process. In order to explore the salient photodynamics of such oligo-PE gold(I) complexes effectively, we have deliberately chosen three model complexes, namely, Ph-C≡C-Au(PMe3) (1a') and Ph-C≡C-(1,m)C6H4-C≡C-Au(PMe3) (m=4, 2a'; m=3, 3a') in place of the real system. Firstly, electronic structure methods based on DFT and TD-DFT are utilized to perform optimization calculations for the ground- and lowest-lying excited states, respectively. Next, basic photophysical properties including absorption and emission spectra are investigated by TD-DFT under the optimized geometries. Besides, on the basis of the electronic spectra herein, we succeed in searching for surface intersections as the minima on the seam of singlet-triplet surface crossings (SCs) at the CASSCF level of theory. By integration of the results available, the process of delayed fluorescence of triplet-triplet annihilation (TTA) and phosphorescence was displayed in detail with SCs playing the lead in monitoring the ISC.

Influence of primary and auxiliary ligand on spectroscopic properties and luminescent efficiency of organoplatinum(II) complexes bearing functionalized cyclometalated C

A theoretical investigation into eighteen recently synthesized Pt(ii) complexes [(R1(n)-C^N^C-R2(n))Pt(L)] with doubly deprotonated cyclometalated R1(n)-C^N^C-R2(n) ligands (n = 1-9, R1(n)-C^N^C-R2(n) = 2,6-diphenylpyridine derivatives) and L ligands (L = DMSO, 1-9; L = -C[triple bond, length as m-dash]N-Ar, 1a-9a), which are used as emitters in orange-red emitting diodes, is reported in this paper. Geometric and electronic structures, absorption and emission spectra, phosphorescence quantum yields, and electroluminescence (EL) efficiency were investigated by DFT and TDDFT methods. We focused on the influence of the primary ligand (R1(n)-C^N^C-R2(n)) and auxiliary ligand (L) on the optical and electronic properties of Pt(ii) complexes by introducing carbazole, fluorene, and thiophene group in the primary ligand and/or the replacement of DMSO by -C[triple bond, length as m-dash]N-Ar as an ancillary ligand. The incorporation of carbazole, fluorene, and thiophene into the primary ligand caused the red-shift of absorption and emission spectra. The metal-ligand bond length is contracted where -C[triple bond, length as m-dash]N-Ar was employed as the secondary ligand, which facilitate the metal to ligand charge transfer (MLCT). The larger involvement of MLCT character in emission process is beneficial for improving the quantum yields of 2a-9a. For EL efficiency, all the complexes have a good balance of reorganization energy as potential systems for fabricating effective OLEDs devices except for 1 and 1a. In addition, two new molecules were designed with comparable or better EL efficiency.

Theoretical investigations of the structures and electronic spectra of Zn(II) and Ni(II) complexes with cyclohexylamine-N-dithiocarbamate.

The ground-state structures of two ligands cyclohexylamine-N-dithiocarbamate (L) and PPh3 and four complexes [Zn(L)2] (A), [Ni(L)2] (B), [Zn(L)2PPh3] (C), and [Ni(L)2PPh3] (D) are optimized by M06, B3LYP, and B3PW91 methods with the same mixed basis set. As compared with the experimental data of other complexes containing the Ni-P bond, the result obtained by M06/6-31+G(d)-LANL2DZ method is finally regarded as accurate and reliable for this project. Based on the optimized geometries, the compositions of molecular orbitals are analyzed and the absorption spectra are simulated. When one more ligand PPh3 is coordinated, the lowest-lying transition energy presents red-shift; while it shows blue-shift when the metal coordination center change from Ni to Zn with the same ligands. The detailed transition characters related with the absorption spectrum are assigned. In all the key transitions, it is hard to find the contribution from Zn atom. On the contrary, the d orbital of Ni atom contributes a lot for the HOMO and LUMO of complexes B and D. Consequently, the transition characters of Zn(II) and Ni(II) complexes are different.

The reasons for ligand-dependent quantum yields and spectroscopic properties of platinum(II) complexes based on tetradentate O

DFT and TD-DFT methods have been employed to theoretically investigate the properties of three recently synthesized green-emitting platinum(II) complexes (1-3) bearing tetradentate O^N^C^N ligands (O^C^N^C = 2-(4-(3,5-di-tert-butylphenyl)-6-(3-(pyridin-2-yl)phenyl)-pyridin-2-yl)phenolate and its derivatives) that have been testified to be good emitters in organic light-emitting diodes (OLEDs), especially for complex 3. The effect of the variation of the substituents on the electronic and optical properties is emphatically explored. Our calculation results reveal that the introduction of an electron-releasing group on one phenyl ring of the O^C^N^C ligand (complex 2) does not result in a distinct alteration of the spectra. However, the incorporation of the norbornane group to the O^C^N^C ligand (complex 3) leads to a blue-shift in the absorption and emission spectra as compared with 1. In addition, how the absorption and emission spectra are affected by the solvent polarity is studied. Both the absorption and the emission spectra display red-shifts of various degrees with the decrease of the solvent polarity. The different phosphorescent quantum yields of the three complexes are compared. It is reasonable to believe that the high (3)MLCT (metal-to-ligand charge transfer) contribution and high percentage of the metallic character (M(c), %) in the emission process, as well as the largest vertical transition energy for 3, result in the highest quantum efficiency.

Understanding the interaction between valsartan and detergents by NMR techniques and molecular dynamics simulation.

Valsartan (VST) is one of the Angiotensin II receptor antagonists, which is widely used in clinical hypertension treatment. It is believed that VST incorporates into biological membranes before it binds to AT(1) receptor. Herein the interactions between VST and detergents, mimicking the membrane environment, were investigated by using nuclear magnetic resonance (NMR) techniques and molecular dynamics (MD) simulation. We observed that VST has two conformers (trans and cis) exchanging slowly in DPC (dodecyl-phosphocholine) micelles, a widely used detergent. The changes of chemical shifts, relaxation rates, and self-diffusion coefficients of VST protons indicate that both conformers have strong interactions with DPC. NOE cross peaks and MD simulation reveal that DPC interacts with VST not only through the hydrophobic lipid chain, but also the hydrophilic headgroup, locating VST at the charged headgroup and upper part of the micelles. Our results are in good agreement with the Raman spectroscopic studies of VST in the DPPC (dipalmitoyl-phosphatidylcholine) bilayers by Potamitis et al. (Biochim. Biophys. Acta. 2011). The concentration ratio of trans over cis conformers is 0.94, showing that two conformers have the same affinities with the detergent, which is significantly smaller than our previous results obtained in SDS (sodium dodecyl sulfate) micelles. MD simulation suggested that the cis conformer has slightly lower binding free energy than the trans conformer when interacting with DPC. The conformational change of VST was further investigated in two detergents, CTAB (hexadecyltrimethylammonium bromide) and Tween-20 (polysorbate 20). Ratios of conformer A and B in the presence of detergents are in the order of DPC, CTAB < Tween-20 < SDS, which is correlated with the charge characters of their head groups. NMR investigations and MD simulations indicate that the electrostatic interaction plays an essential role in the binding process of VST with detergents, and the hydrophobic interaction influences the packing of the drug in the micelles. These results may be of help in understanding delivery processes of sartan drugs in cell membranes.

Hydrogen abstraction reactions of OH radicals with CH3CH2CH2Cl and CH3CHClCH3: a mechanistic and kinetic study.

The hydrogen abstraction reactions of OH radicals with CH3CH2CH2Cl and CH3CHClCH3 (R2) have been investigated theoretically by a dual-level direct dynamics method. The optimized geometries and frequencies of the stationary points are calculated at the B3LYP/6-311G(d,p) level. To improve the reaction enthalpy and potential barrier of each reaction channel, the single point energy calculation is performed by the BMC-CCSD method. Using canonical variational transition-state theory (CVT) with the small-curvature tunneling correction, the rate constants are evaluated over a wide temperature range of 200-2000 K at the BMC-CCSD//B3LYP/6-311G(d,p) level. For the reaction channels with the negative barrier heights, the rate constants are calculated by using the CVT. The calculated total rate constants are consistent with available experimental data. The results show that at lower temperatures, the tunneling correction has an important contribution in the calculation of rate constants for all the reaction channels with the positive barrier heights, while the variational effect is found negligible for some reaction channels. For reactions OH radicals with CH3CH2CH2Cl (R1) and CH3CHClCH3 (R2), the channels of H-abstraction from -CH2 - and -CHCl groups are the major reaction channels, respectively, at lower temperatures. With temperature increasing, contributions from other channels should be taken into account. Finally, the total rate constants are fitted by two models, i.e., three-parameter and four-parameter expressions. The enthalpies of formation of the species CH3CHClCH2, CH3CHCH2Cl, and CH3CH2CH2Cl are evaluated by isodesmic reactions.

Identifying Tm@C82 isomers with density functional theory calculations.

Density functional theory calculations have been performed to study the geometrical and electronic properties of endohedral metallofullerene Tm@C(82) isomers. Three energetically favorable isomers (with C(s), C(2) and C(2v) symmetry, respectively) are identified which are consistent with the nuclear magnetic resonance (NMR) observations. The simulated ultraviolet photoelectron spectra (UPS) based on the three structures agree well with the measurements. Particularly, the parent cage of the experimentally observed Tm@C(82) isomer with C(s) symmetry is newly assigned, which matches the experiments better than early assignments. In addition, strong interaction between an endohedral Tm atom and the C(82) cage is discussed and is thought to be responsible for the dramatic change in the relative stability of C(82) isomers when Tm is encapsulated.

Direct Ab initio dynamics study on the reaction of CH3CHF2 (HFC-152a) with the Cl atom.

A direct ab initio dynamics method is used to investigate the hydrogen-abstraction reaction CH(3)CHF(2)+Cl. One transition state is located for alpha-H abstraction, and two are identified for beta-H abstraction. The potential-energy surface (PES) is obtained at the G3(MP2)//MP2/6-311G(d, p) level. Furthermore, the rate constants of the three channels are evaluated by using canonical variational transition-state theory (CVT) with small-curvature tunneling (SCT) contributions over a wide temperature range of 200-2500 K. The dynamic calculations show that the reaction proceeds mainly by alpha-H abstraction over the whole temperature range. The calculated rate constants and branching ratios are both in good agreement with the available experimental values.

Theoretical study of the reactions CF3CH2OCHF2 + OH/Cl and its product radicals and parent ether(CH3CH2OCH3) with OH.

A dual-level direct dynamic method is employed to study the reaction mechanisms of CF3CH2OCHF2 (HFE-245fa2; HFE-245mf) with the OH radicals and Cl atoms. Two hydrogen abstraction channels and two displacement processes are found for each reaction. For further study, the reaction mechanisms of its products (CF3CH2OCF2 and CF3CHOCHF2) and parent ether CH3CH2OCH3 with OH radical are investigated theoretically. The geometries and frequencies of all the stationary points and the minimum energy paths (MEPs) are calculated at the B3LYP/6-311G(d,p) level. The energetic information along the MEPs is further refined at the G3(MP2) level of theory. For reactions CF3CH2OCHF2 + OH/Cl, the calculation indicates that the hydrogen abstraction from --CH2-- group is the dominant reaction channel, and the displacement processes may be negligible because of the high barriers. The standard enthalpies of formation for the reactant CF3CH2OCHF2, and two products CF3CH2OCHF2 and CF3CHOCHF2 are evaluated via group-balanced isodesmic reactions. The rate constants of reactions CF3CH2OCHF2 + OH/Cl and CH3CH2OCH3 + OH are estimated by using the variational transition state theory over a wide range of temperature (200-2000 K). The agreement between the theoretical and experimental rate constants is good in the measured temperature range. From the comparison between the rate constants of the reactions CF3CH2OCHF2 and CH3CH2OCH3 with OH, it is shown that the fluorine substitution decreases the reactivity of the C--H bond.

Theoretical study for the reaction of CH3OCl with Cl atom.

A direct dynamics method is employed to study the kinetics of the multiple channel reaction CH(3)OCl + Cl. The potential energy surface (PES) information is explored from ab initio calculations. Two reaction channels, Cl- and H-abstractions, have been identified. The optimized geometries and frequencies of the stationary points and the minimum-energy paths (MEPs) are calculated at the MP2 level of theory using the 6-311G(d, p) and cc-pVTZ basis sets, respectively. The single-point energies along the MEPs are further refined at the G3(MP2)//MP2/6-311G(d, p), G3//MP2/6-311G(d, p), as well as by the multicoefficient correlation method based on QCISD (MC-QCISD) using the MP2/cc-pVTZ geometries. The enthalpies of formation for the species CH(3)OCl and CH(2)OCl are calculated via isodesmic reactions. The rate constants of the two reaction channels are evaluated by using the variational transition-state theory over a wide range of temperature, 220-2200 K. The calculated rate constants exhibit the slightly negative temperature dependence and show good agreement with the available experimental data at room temperature at the G3(MP2)//MP2/6-311G(d, p) level. The present calculations indicate that the two channels are competitive at low temperatures while H-abstraction plays a more important role with the increase of temperature. The calculated k(1a)/k(1) ratio of 0.5 at 298 K is in general agreement with the experimental one, 0.8 +/- 0.2. The high rate constant for CH(3)OCl + Cl shows that removal by reaction with Cl atom is a potentially important loss process for CH(3)OCl in the polar stratosphere.

Direct ab initio dynamics calculation of the reaction rates of CH3OCl with OH.

A direct ab initio dynamics method was carried out for the reaction CH3OCl + OH --> products. Three abstraction channels from chlorine atom, in-plane hydrogen, and out-of-plane hydrogen atoms at the CH3 group have been found. The optimized geometries and frequencies of the stationary points and the minimum-energy paths (MEPs) were calculated at the MP2/6-311G(d,p) level. To improve the reaction enthalpy and potential barrier, single-point calculations were made at three higher levels of theory, the approximate QCISD(T)/6-311++G(3df,2pd), G3, and G3(MP2) levels. Furthermore, the rate constants for three abstraction channels were evaluated using canonical variational transition state theory (CVT) with the small-curvature tunneling correction (SCT) over a wide temperature range of 220-2000 K at above three higher theory levels, respectively. The calculated rate constants as well as branching rates are in reasonable agreement with the experimental values in the temperature region 250-341 K. The present results indicate H-abstraction especially from out-of-plane hydrogen is the main reaction pathway, while Cl-abstraction is much less competitive.