Charge Recombination in Phosphorescent Organic Light-Emitting Diode Host–Guest Systems through QM/MM Simulations

The Journal of Physical Chemistry C
Host–guest systems are crucial for achieving high efficiency in most organic light-emitting diode (OLED) devices. However, charge recombination in such systems is poorly understood due to complicated molecular environment, making the rational design of host–guest systems difficult. In this article, we present a computational study of a phosphorescent OLED with 2,8-bis(triphenylsilyl)dibenzofuran (BTDF) as the host and fac-tris(2-phenylpyridine) iridium (fac-Ir(ppy)3) as the guest, using a combined quantum mechanics/molecular mechanics (QM/MM) scheme. A new reaction coordinate is introduced to measure the electrostatic interactions between the host and guest molecules. Ionization potentials and electron affinities of the host show broader distributions as the host–guest interaction increases. On the basis of these distributions, we describe a molecular picture of charge recombination on the guest and find a direct charge trapping route for this system....  Read more

Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects

Journal of the American Chemical Society
Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction’s transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured...  Read more

Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations

Biochemistry
The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem–OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.Read more

First hyperpolarizability of para-aminoaniline induced by a variety of gold nano particles

Physical Chemistry Chemical Physics
Molecules exposed to an electromagnetic field due to the presence of nearby nanoparticles are known to be affected. The nonlinear response of the molecular system, the first hyperpolarizability, is investigated for 4-nitroaniline (PNA) in a variety of different nanoparticle environments. In order to introduce different molecular environments the quantum mechanical–molecular mechanics DFT/MM response method was utilized for calculating the electromagnetic properties of the molecule interacting with the nanoparticles and the frequency dependent electromagnetic fields. We clearly show that the metal nanoparticles are able to influence the first hyperpolarizability of the molecule, and that the influence strongly depends on the chosen molecular environment. It is found that the first hyperpolarizability of the molecule strongly depends on the distance and orientation to the nanoparticles, whereas the size of the nanoparticles is of little importance when a sufficiently sized...  Read more

Computational Analysis of Sterol Ligand Specificity of the Niemann Pick C2 Protein

Biochemistry
Transport of cholesterol derived from hydrolysis of lipoprotein associated cholesteryl esters out of late endosomes depends critically on the function of the Niemann Pick C1 (NPC1) and C2 (NPC2) proteins. Both proteins bind cholesterol but also various other sterols and both with strongly varying affinity. The molecular mechanisms underlying this multiligand specificity are not known. On the basis of the crystal structure of NPC2, we have here investigated structural details of NPC2–sterol interactions using molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculations. We found that an aliphatic side chain in the sterol ligand results in strong binding to NPC2, while side-chain oxidized sterols gave weaker binding. Estradiol and the hydrophobic amine U18666A had the lowest affinity of all tested ligands and at the same time showed the highest flexibility within the NPC2 binding pocket. The binding affinity of all ligands correlated highly with their calculated...  Read more

A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B

Journal of Chemical Information and Modeling
The discovery of unique substrates is important for developing potential applications of enzymes. However, the experimental procedures for substrate identification are laborious, time-consuming, and expensive. Although in silico structure-based approaches show great promise, recent extensive studies have shown that these approaches remain a formidable challenge for current biocomputational methodologies. Here we present an open-source, extensible, and flexible software platform for predicting enzyme substrates called THEMIS, which performs in silico virtual screening for potential catalytic targets of an enzyme on the basis of the enzyme’s catalysis mechanism. On the basis of a generalized transition state theory of enzyme catalysis, we introduce a modified docking procedure called “mechanism-based restricted docking” (MBRD) for novel substrate recognition from molecular docking. Comprising a series of utilities written in C/Python, THEMIS automatically executes...  Read more

Spectroscopy and dynamics of double proton transfer in formic acid dimer

Physical Chemistry Chemical Physics
We present the isolated gas phase infrared spectra of formic acid dimer, (HCOOH)2, and its deuterated counterpart formic-d acid, (DCOOH)2, at room temperature. The formic acid dimer spectrum was obtained by spectral subtraction of a spectrum of formic acid vapor recorded at low pressure from that recorded at a higher pressure. The spectra of formic acid vapor contain features from both formic acid monomer and formic acid dimer, but at low and high pressures of formic acid, the equilibrium is pushed towards the monomer and dimer, respectively. A similar approach was used for the formic-d acid dimer. Building on the previous development of the Molecular Mechanics with Proton Transfer (MMPT) force field for simulating proton transfer reactions, molecular dynamics (MD) simulations were carried out to interpret the experimental spectra in the OH-stretching region. Within the framework of MMPT, a combination of symmetric single and double...  Read more

Solvent effects on the properties of hyperbranched polythiophenes

Physical Chemistry Chemical Physics
The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches...  Read more

Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy

ACS Nano
Scanning tunneling microscopy and atomic force microscopy can provide detailed information about the geometric and electronic structure of molecules with submolecular spatial resolution. However, an essential capability to realize the full potential of these techniques for chemical applications is missing from the scanning probe toolbox: chemical recognition of organic molecules. Here, we show that maps of the minima of frequency shift–distance curves extracted from 3D data cubes contain characteristic contrast. A detailed theoretical analysis based on density functional theory and molecular mechanics shows that these features are characteristic for the investigated species. Structurally similar but chemically distinct molecules yield significantly different features. We find that the van der Waals and Pauli interaction, together with the specific adsorption geometry of a given molecule on the surface, accounts for the observed contrast.Read more

New Mechanistic Pathways for Criegee–Water Chemistry at the Air/Water Interface

Journal of the American Chemical Society
Understanding Criegee chemistry has become one of central topics in atmospheric research recently. The reaction of Criegee intermediates with gas-phase water clusters has been widely viewed as a key Criegee reaction in the troposphere. However, the effect of aerosols or clouds on Criegee chemistry has received little attention. In this work, we have investigated the reaction between the smallest Criegee intermediate, CH2OO, and water clusters in the gas phase, as well as at the air/water surface using ab initio quantum chemical calculations and adaptive buffered force quantum mechanics/molecular mechanics (QM/MM) dynamics simulations. Our simulation results show that the typical time scale for the reaction of CH2OO with water at the air/water interface is on the order of a few picoseconds, 2–3 orders of magnitude shorter than that in the gas phase. Importantly, the adbf-QM/MM dynamics simulations suggest several reaction pathways for the CH2OO +...  Read more

Two-Dimensional Supramolecular Polymers Embodying Large Unilamellar Vesicles in Water

Journal of the American Chemical Society
We hereby describe a strategy for obtaining novel topological nanostructures consisting of dual-cavity basket 1, forming a curved monolayer of large unilamellar vesicles in water (CAC < 0.25 μM), and bivalent guests 4/5 populating the cavities of such bolaamphiphilic hosts. On the basis of the results of 1H NMR spectroscopy, electron microscopy, and dynamic light scattering measurements, we postulated that divalent guest molecules 4/5 cover the curved vesicular surface in a lateral fashion to satisfy the complexation [2 + 2] valency and thereby give stable two-dimensional supramolecular polymers [14]n and [15]n. The results of experimental studies are also supported with coarse-grained molecular dynamics simulations and molecular mechanics. Our discovery about the assembly of novel vesicular structures could be of interest for stabilization/functionalization of liposomal surfaces...  Read more

How Do Distance and Solvent Affect Halogen Bonding Involving Negatively Charged Donors?

The Journal of Physical Chemistry B
It was reported that negatively charged donors can form halogen bonding, which is stable, especially, in a polar environment. On the basis of a survey of the Protein Data Bank, we noticed that the distance between the negative charge center and the halogen atom of an organohalogen may vary greatly. Therefore, a series of model systems, composed of 4-halophenyl-conjugated polyene acids and ammonia, were designed to explore the potential effect of distance on halogen bonding in different solvents. Quantum mechanics (QM) calculations demonstrated that the longer the distance, the stronger the bonding. The energy decomposition analysis on all of the model systems demonstrated that electrostatic interaction contributes the most (44–56%) to the overall binding, followed by orbital interaction (42–36%). Natural bond orbital calculations showed that electron transfer takes place from the acceptor to the donor, whereas the halogen atom becomes more positive during the bonding, which is in...  Read more

Theoretical Modeling of the Chirality Discrimination of Enantiomers by Nanotubular Cyclic Peptides using Gas-Phase Photoelectron Spectroscopy: An ONIOM Spectroscopic Calculations

The Journal of Physical Chemistry A
In the present work, the chirality recognition of the enantiomers of a chiral molecule (1-phenyl-1-propanol) interacting with a nanotubular cyclic peptide (E-type cyclic decapeptide) was investigated by their ionization in the gas phase, theoretically. The absolute energy difference between the interaction of the S- and R-enantiomer with the cyclic peptide, calculated at the M06-2X/6-311++G(d, p) level of theory, was 4.70 kcal·mol–1. Two different schemes of “Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)” method such as (quantum mechanics (QM):molecular mechanics (MM)) and (QM:QM) were employed to study the effect of the interaction on the gas-phase ionization energies of the enantiomers and cyclic peptide, separately. The symmetry-adapted cluster/configuration interaction (SAC-CI) methodology was used for the calculation of the ionization energies. It was found that the difference between the interactions of R- and S-enantiomer with...  Read more

Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations

Journal of Chemical Theory and Computation
The coenzyme nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH) play ubiquitous roles as oxidizing and reducing agents in nature. The binding, and possibly the chemical redox step, of NAD+/NADH may be influenced by the cofactor conformational distribution and, in particular, by the ribose puckering of its nicotinamide–ribonucleoside (NR) moiety. In many hybrid quantum mechanics–molecular mechanics (QM/MM) studies of NAD+/NADH dependent enzymes, the QM region is treated by semiempirical (SE) methods. Recent work suggests that SE methods do not adequately describe the ring puckering in sugar molecules. In the present work we adopt an efficient and practical strategy to correct for this deficiency for NAD+/NADH. We have implemented a cost-effective correction to a SE Hamiltonian by adding a correction potential, which is defined as the difference between an accurate benchmark density functional theory (DFT) potential...  Read more

Dehydration of Methanediol in Aqueous Solution: An ONIOM(QM/MM) Study

The Journal of Physical Chemistry A
We used ONIOM(QM/MM) method to examine the dehydration of a methanediol in aqueous solution. A methanediol and a small number of water molecules in the proximity of the methanediol are calculated with quantum mechanics (QM), while a number of water molecules far from the methanediol are calculated with molecular mechanics (MM). A molecular dynamical simulation shows that 12 water molecules are located within the hydration shell of a methanediol. The energy barrier for the dehydration of a methanediol decreases when we increase the number of water molecules in the QM region and converges toward a finite value when 12 water molecules are included in the QM region. This indicates a significant effect of water molecules within the hydration shell on the dehydration process of a methanediol in aqueous solution. The dehydration rate calculated with the ONIOM(QM/MM) method agrees well with that obtained from a laboratory experiment.Read more

Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra

The Journal of Physical Chemistry C
Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is...  Read more

The Effect of Core Correlation on the MP2 Hydration Free Energies of Li+, Na+, and K+

The Journal of Physical Chemistry B
Simple nonpolarizable molecular mechanics potentials were developed for Li+, Na+, and K+ with the adaptive force matching (AFM) method using the second order Møller–Plesset perturbation theory (MP2) with the frozen core approximation as reference. The effects of different choices of core orbitals and basis sets in the MP2 calculations were investigated for Na+ and Li+. For Na+, correlating the 2s2p electrons in MP2 changes its hydration free energy by 18 kJ/mol, which is surprisingly large, constituting to about 5% of the intrinsic hydration free energy of the ion. Whereas correlating the 2s2p electrons with the aug-cc-pCVTZ basis set leads to the best agreement with experiments, with the aug-cc-pVTZ basis set, a better hydration free energy will be obtained if the 2s2p are kept as frozen core orbitals. Even with nonpolarizable energy expressions, the AFM derived ion potentials predict the experimental hydration free...  Read more

Simulation of Singlet Exciton Diffusion in Bulk Organic Materials

Journal of Chemical Theory and Computation
We present a scheme for nonadiabatic direct dynamics simulation of Frenkel exciton diffusion in bulk molecular systems. The fluctuations of exciton couplings caused by the molecular motion can crucially influence exciton transport in such materials. This effect can be conveniently taken into account by computing the exciton couplings along molecular dynamics trajectories, as shown recently. In this work, we combine Molecular Dynamics simulations with a Frenkel Hamiltonian into a combined quantum-mechanical/molecular mechanics approach in order to allow for a simultaneous propagation of nuclear and electronic degrees of freedom using nonadiabatic dynamics propagation schemes. To reach the necessary time and length scales, we use classical force-fields and the semiempirical time-dependent density functional tight-binding method in combination with a fragmentation of the electronic structure. Fewest-switches surface-hopping, with adaptions to handle trivial crossings, and the...  Read more

Two Binding Geometries for Risperidone in Dopamine D3 Receptors: Insights on the Fast-Off Mechanism through Docking, Quantum Biochemistry, and Molecular Dynamics Simulations

ACS Neuroscience
Risperidone is an atypical antipsychotic used in the treatment of schizophrenia and of symptoms of irritability associated with autism spectrum disorder (ASD). Its main action mechanism is the blockade of D2-like receptors acting over positive and negative symptoms of schizophrenia with small risk of extrapyramidal symptoms (EPS) at doses corresponding to low/moderate D2 occupancy. Such a decrease in the side effect incidence can be associated with its fast unbinding from D2 receptors in the nigrostriatal region allowing the recovery of dopamine signaling pathways. We performed docking essays using risperidone and the D3 receptor crystallographic data and results suggested two possible distinct orientations for risperidone at the binding pocket. Orientation 1 is more close to the opening of the binding site and has the 6-fluoro-1,2 benzoxazole fragment toward the bottom of the D3 receptor cleft, while orientation 2 is deeper inside the binding pocket with the same fragment toward to...  Read more

Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II

Biochemistry
Ammonia binds to two sites in the oxygen-evolving complex (OEC) of Photosystem II (PSII). The first is as a terminal ligand to Mn in the S2 state, and the second is at a site outside the OEC that is competitive with chloride. Binding of ammonia in this latter secondary site results in the S2 state S = 5/2 spin isomer being favored over the S = 1/2 spin isomer. Using electron paramagnetic resonance spectroscopy, we find that ammonia binds to the secondary site in wild-type Synechocystis sp. PCC 6803 PSII, but not in D2-K317A mutated PSII that does not bind chloride. By combining these results with quantum mechanics/molecular mechanics calculations, we propose that ammonia binds in the secondary site in competition with D1-D61 as a hydrogen bond acceptor to the OEC terminal water ligand, W1. Implications for the mechanism of ammonia binding via its primary site directly to Mn4 in the OEC are discussed.Read more