Insights into uranyl chemistry from molecular dynamics simulations

First-principles and purely classical molecular dynamics (MD) simulations for complexes of the uranyl ion (UO(2)(2+)) are reviewed. Validation of Car-Parrinello MD simulations for small uranyl complexes in aqueous solution is discussed. Special attention is called to the mechanism of ligand-exchange reactions at the uranyl centre and to effects of solvation and hydration on coordination and structural properties. Large-scale classical MD simulations are surveyed in the context of liquid-liquid extraction, with uranyl complexes ranging from simple hydrates to calixarenes, and nonaqueous phases from simple organic solvents and supercritical CO(2) to ionic liquids.     

Fluorescence up-conversion study of excitation energy transport dynamics in oligothiophene-fullerene linked dyads

Photoinduced excitation energy transport dynamics in oligothiophene-fullerene linked dyads, nT-C60 (n = 4, 8, and 12), have been investigated by femtosecond fluorescence up-conversion. In 8T-C60 and 12T-C60, each time profile of the fluorescence due to the 1nT* moiety consists of two components. The sub-picosecond component and a few picosecond components were experimentally evaluated depending on the lengths of oligothiophenes (n =8 and 12) and on the analyzing wavelength of the fluorescence. However, the time trace of the fluorescence due to 14T*-C60 decayed with a single short component in approximately 300 fs due to direct excited energy transfer (EET) from the 14T* moiety to the C60 moiety. On the basis of the kinetic models considering the short and long locally pi-conjugative thiophene segments in 8T-C60 and 12T-C60, the rate parameters of the elemental processes were evaluated. Sub-picosecond time constants of nT-C60 were found to be EET from the thiophene segment vicinal to the C60 moiety and intrachain energy transfer. Slower picosecond dynamics mainly corresponds to EET from the thiophene segments apart from the C60 moiety.     

Coordinative-to-covalent transformation,isomerization dynamics,and logic gate application of dithienylethene based photochromic cages

Photochromic coordinative cages containing dynamic C N imine bonds are assembled from a dithienylethene-based aldehyde and tris-amine precursors via metallo-component self-assembly. The resulting metal-templated cages are then reduced and demetalated into pure covalent-organic cages (COCs), which are otherwise difficult to prepare via de novo organic synthesis. Both the obtained coordinative and covalent cages can be readily interconverted between the ring-open (o-isomer) and one-lateral ring-closed (c-isomer) forms by UV/vis light irradiation, demonstrating distinct absorption, luminescence and photoisomerization dynamics. Specifically, the ring-closed c-COCs show a blue-shifted absorption band compared with analogous metal-templated cages, which can be applied in photoluminescence (PL) color-tuning of upconversion materials in different ways, showing potential for constructing multi-readout logic gate systems.

Metal-templated component self-assembly and then demetalation affords photochromic covalent organic cages applicable for upconversion PL-color tuning for logic gates.     

Insights into photodissociation dynamics of propionyl chloride from ab initio calculations and molecular dynamics simulations

The potential energy surfaces of isomerization, dissociation, and elimination reactions for CH3CH2COCl in the S0 and S1 states have been mapped with the different ab initio calculations. Mechanistic photodissociation of CH3CH2COCl at 266 nm has been characterized through the computed potential energy surfaces, the optimized surface crossing structure, intrinsic reaction coordinate, and ab initio molecular dynamics calculations. Photoexcitation at 266 nm leads to the CH3CH2COCl molecules in the S1 state. From this state, the C-Cl bond cleavage proceeds in a time scale of picosecond in the gas phase. The barrier to the C-Cl bond cleavage on the S1 surface is significantly increased by effects of the matrix and the internal conversion to the ground state prevails in the condensed phase. The HCl eliminations as a result of internal conversion to the ground state become the dominant channel upon photodissociation of CH3CH2COCl in the argon matrix at 10 K.     

Insights into photodissociation dynamics of benzamide and formanilide from ab initio calculations

In the present study, the five lowest electronic states that control the UV photodissociation of formanilide and benzamide have been characterized using the complete active space self-consistent field theory. The mechanisms for the initial relaxation and subsequent dissociation processes have been determined on the basis of the calculated potential energy surfaces and their intersections. It was found that the S(1)/T(1)/T(2) three-surface intersection plays an important role in the photodissociation processes of benzamide. However, the dissociation behavior of formanilide and benzamide was found to be quite different from that for aliphatic amides. The present study provides several insights into the photodissociation dynamics of formanilide and benzamide.     

Insights into dynamics of the S2 state of thiophosgene from ab initio calculations

The S2 potential energy surface for Cl2CS dissociation has been characterized with a combined complete active space self-consistent field and multireference configuration interaction method. The S3/S2 minimum-energy intersection has been determined with the state-averaged complete active space self-consistent field method. The S2 direct dissociation was found to have a barrier of 6.0 kcal/mol, leading to formation of Cl(X2P)+ClCS(A2A") in the excited electronic state. Dynamics of the S2 state of Cl2CS can be summarized as follows: (1) The S2-S0 fluorescence occurs with high quantum yield at low excess energies; (2) Both the S(2) dissociation and the S2-->S3 internal conversion cause the loss of the S2-S0 fluorescence upon photoexcitation at 235-253 nm; (3) The S2-->S3 internal conversion (IC) followed by the direct IC to the ground electronic state results in the fragments produced in the ground state, while the S2 dissociation leads to formation of the fragments in excited electronic states.     

Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations

DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linked dinucleotides. The detailed structure of the damaged DNA macromolecule has remained elusive. In this study we generated in silico the most frequent oxidative intrastrand cross-link adduct, G[8,5-Me]T, embedded in a solvated DNA dodecamer by means of quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations. The free energy of activation required to bring the reactant close together and to form the C-C covalent-bond is estimated to be ~10 kcal/mol. We observe that the G[8,5-Me]T tandem lesion is accommodated with almost no perturbation of the Watson-Crick hydrogen-bond network and induces bend and unwinding angles of ~20° and 8°, respectively. This rather small structural distortion of the DNA macromolecule compared to other well characterized intrastrand cross-links, such as cyclobutane pyrimidines dimers or cisplatin-DNA complex adduct, is a probable rationale for the known lack of efficient repair of oxidative damages.     

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations

The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the mechanism of substrate binding. We develop a kinetic network model, constructed from detailed atomistic simulations, to determine the kinetic mechanisms of the conformational transitions in HIV-1 PR. To overcome the time scale limitation of conventional molecular dynamics (MD) simulations, our method combines replica exchange MD with transition path theory (TPT) to study the diversity and temperature dependence of the pathways connecting functionally important states of the protease. At low temperatures the large-scale flap opening is dominated by a small number of paths; at elevated temperatures the transition occurs through many structurally heterogeneous routes. The expanded conformation in the crystal structure 1TW7 is found to closely mimic a key intermediate in the flap-opening pathways at low temperature. We investigated the different transition mechanisms between the semi-open and closed forms. The calculated relaxation times reveal fast semi-open ? closed transitions, and infrequently the flaps fully open. The ligand binding rate predicted from this kinetic model increases by 38-fold from 285 to 309 K, which is in general agreement with experiments. To our knowledge, this is the first application of a network model constructed from atomistic simulations together with TPT to analyze conformational changes between different functional states of a natively folded protein.     

Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg(2)ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp(166), as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp(166) is short and dynamically stable, whereas the QM study indicates that an Asp(166)-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.     

Excited-state energy-transfer dynamics of self-assembled imine-linked porphyrin dyads

Toward the development of new strategies for the synthesis of multiporphyrin arrays, we have prepared and characterized (electrochemistry and static/time-resolved optical spectroscopy) a series of dyads composed of a zinc porphyrin and a free base porphyrin joined via imine-based linkers. One dyad contains two zinc porphyrins. Imine formation occurs under gentle conditions without alteration of the porphyrin metalation state. Five imine linkers were investigated by combination of formyl, benzaldehyde, and salicylaldehyde groups with aniline and benzoic hydrazide groups. The imine-linked dyads are quite stable to routine handling. The excited-state energy-transfer rate from zinc to free base porphyrin ranges from (70 ps)(-)(1) to (13 ps)(-)(1) in toluene at room temperature depending on the linker employed. The energy-transfer yield is generally very high (>97%), with low yields of deleterious hole/electron transfer. Collectively, this work provides the foundation for the design of multiporphyrin arrays that self-assemble via stable imine linkages, have predictable electronic properties, and have comparable or even enhanced energy-transfer characteristics relative to those of other types of covalently linked systems.     

Formation of selectivity in molecular isomerization by the IR multiphoton excitation

The formation mechanism of the selectivity of IR laser isomerization induced by vibrational multiphoton excitation is considered. The effective and highly selective isomerization of perfluorodimethyl ketene (CF₃)₂C=C=O into perfluoromethacrylic acid fluoride F₂C=C(CF₃)COF and perfluorocyclobutene into perfluorobutadiene upon pulse irradiation with a CO₂ laser and its second harmonic was performed. The conversion of (CF₃)₂C=C=O into F₂C=C(CF₃)COF was higher than 99%. A record-breaking conversion of 99.8% of the parent substance into the isomer was achieved in the case of perfluorocyclobutene isomerization into perfluorobutadiene. It was shown that the high selectivity of the laser-induced chemical reactions is mainly associated with the different levels of the vibrational excitation of the parent molecules and their isomers. The latter is due to the difference in the IR absorption spectra of different isomers, which allows for the excitation of the necessary component with a high selectivity.     

Insights into mechanistic photodissociation of chloroacetone from a combination of electronic structure calculation and molecular dynamics simulation

The stationary and intersection structures on the S(0) and S(1) potential energy surfaces of CH(3)COCH(2)Cl have been determined by the CAS(10,8)/cc-pVDZ optimizations and their relative energies are refined by the CASPT2//CAS(10,8)/cc-pVDZ single-point calculations. Non-adiabatic molecular dynamics simulations were performed on the basis of the state-averaged CAS(10,8)/cc-pVDZ calculated energies, energy gradients, and Hessian matrix for the S(0) and S(1) states. It is found that the features of the S(1) potential energy surface and non-adiabatic effect control the selectivity of the two α-C-C bond fissions, which provides a reasonable explanation why one α-C-C bond was observed as a primary channel and the other is ruled out even if CH(3)COCH(2)Cl is excited at 193 nm. The β-C-Cl fission is determined to be a dominant channel once the CH(3)COCH(2)Cl molecule is excited to the S(1) state and the β-C-Cl:α-C-C branching ratio is estimated by the RRKM rate theory to be 15:1 at 193 nm, which is overestimated in comparison with the value of ~11:1 inferred experimentally. The present calculation reveals that the α-C-C fission might take place in the ground electronic state as a result of the S(1) → S(0) internal conversion upon photolysis at 308 nm. However, the measured kinetic energy distributions of the α-C-C fission products suggest that the fission does not involve internal conversion to the ground state. To solve this issue, we need to perform non-adiabatic quantum dynamics simulation on accurate S(0), S(1), and S(2) potential energy surfaces, which is still a challenging task currently.     

Insights into sulfinate formation from tosyl hydrazides

Benzylation of 1,2-ditosylhydrazine in DMF under various basic conditions results in a benzyl sulfone via intermediary sulfinate formation, providing new insights and allowing practical conclusions to be drawn. The half-lives of 1,2-ditosylhydrazine and several monotosylated hydrazides with 1,1,3,3-tetramethylguanidine in DMSO have been determined by ¹H NMR spectroscopy and are found to vary from a few minutes to several months. In the course of this work a benzylated, partly detosylated compound has been identified and a 1,1,3,3-tetramethyl guanidine-containing side-product characterized. A contradictory report is also commented on.     

Insights into the dynamics of evaporation and proton migration in protonated water clusters from Large‐scale Born–Oppenheimer direct dynamics

Large‐scale on‐the‐fly Born–Oppenheimer molecular dynamics simulations using recent advances in linear scaling electronic structure theory and trajectory integration techniques have been performed for protonated water clusters around the magic number (H₂O)_nH⁺, for n = 20 and 21. Besides demonstrating the feasibility and efficiency of the computational approach, the calculations reveal interesting dynamical details. Elimination of water molecules is found to be fast for both cluster sizes but rather insensitive to the initial geometry. The water molecules released acquire velocities compatible with thermal energies. The proton solvation shell changes between the well‐known Eigen and Zundel motifs and is characterized by specific low‐frequency vibrational modes, which have been quantified. The proton transfer mechanism largely resembles that of bulk water but one interesting variation was observed. © 2012 Wiley Periodicals, Inc.     

Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin

Herein, we present results from molecular dynamics MD simulations ( approximately 1 ns) of the TEM-1 beta-lactamase in aqueous solution. Both the free form of the enzyme and its complex with benzylpenicillin were studied. During the simulation of the free enzyme, the conformation of the Omega loop and the interresidue contacts defining the complex H-bond network in the active site were quite stable. Most interestingly, the water molecule connecting Glu166 and Ser70 does not exchange with bulk solvent, emphasizing its structural and catalytic relevance. In the presence of the substrate, Ser130, Ser235, and Arg244 directly interact with the beta-lactam carboxylate via H-bonds, whereas the Lys234 ammonium group has only an electrostatic influence. These interactions together with other specific contacts result in a very short distance ( approximately 3 A) between the attacking hydroxyl group of Ser70 and the beta-lactam ring carbonyl group, which is a favorable orientation for nucleophilic attack. Our simulations also gave insight into the possible pathways for proton abstraction from the Ser70 hydroxyl group. We propose that either the Glu166 carboxylate-Wat1 or the substrate carboxylate-Ser130 moieties could abstract a proton from the nucleophilic Ser70.     

A semiclassical molecular dynamics of the photochromic ring-opening reaction of spiropyran

The photochromic ring-opening reaction of spiropyran(SP) has been investigated by a realistic semiclassical dynamics simulation,accompanied by SA3-CASSCF(12 10)/MS-CASPT2 potential energy curves(PECs) of S0–S2.The main simulation results show the dominate pathway corresponds to the ringopening process of trans-SP to form the most stable merocyanine(MC) product.These findings provide more important complementarity for interpreting experimental observations.     

Insights into the interplay between electronic structure and protein dynamics: The case of ubiquitin

A quantum mechanical analysis of an experimental ensemble comprising 128 conformers of the protein ubiquitin has been carried out with the aid of LMO–SCF–COSMO calculations. The permanent dipole moment of the protein fluctuates in the range from 131 to 283 D while the energy-weighted average dipole has a magnitude of 197 D. The HOMO–LUMO energy gap of the conformational ensemble ranges from 7.389 to 8.397 eV and appears to being affected mainly by fluctuations in the HOMO energy. An inspection of the frontier orbitals of the 128 conformers indicates that their localization is not affected by the protein dynamics.     

Insights into Ligand-Protein Binding from Local Mechanical Response

Computational studies of ligand-protein binding are crucial for properly designing novel compounds of potential pharmacological interest. In this respect, researchers are increasingly interested in steered molecular dynamics for ligand-protein binding and unbinding studies. In particular, it has been suggested that analyzing the work profiles along the ligand-protein undocking paths could be fruitful. Here, we propose that small portions of work profiles, termed "local mechanical responses" of the system to a steering force, could serve as a universal measure for capturing relevant information about the system under investigation. Specifically, we first collected a high number of steering trajectories using two biological systems of increasing complexity (i.e., alanine dipeptide and (R)-roscovitine/CDK5 complex). Then, we devised a novel postprocessing tool to be applied to the local mechanical responses, to extract structural information related to the biological processes under investigation. Despite the out-of-equilibrium character of the trajectories, the analysis carried out on the work profiles provided pivotal information about the investigated biological processes. This could eventually be applied to drug design.