Stability of Guest-Incorporated 2D Molecular Networks

The Journal of Physical Chemistry C
Molecular self-assembly, taking advantage of reversible intermolecular interactions, represents an efficient method to prepare ultrathin films exhibiting minimal packing defects. The same protocol seems reasonable to fabricate hybrid monolayers yet typically results in segregated domains. Demonstrated herein is a host–guest concept in which guest molecules are hosted in homogeneously patterned voids at the liquid–solid interface. However, 2D open lattices with low packing densities often suffer poor stability. In this study, the concept is realized by a 2D porous network assembled via 1,3,5-tris(4-carboxyphenyl)benzene (BTB) whose stability is significantly enhanced by hosting spatially matched pentacene or its analogues. The conformal contact between the nearest neighbors optimizes intermolecular interactions. Simulation results of molecular mechanics for a simplified model suggest that the hybrid lattice is about 250 kcal/mol per BTB pore more stable than guests such as coronene...  Read more

Conformation of Pyrene-Labeled Amylose in DMSO Characterized with the Fluorescence Blob Model

Macromolecules
Amylose and poly(methyl acrylate) were randomly labeled with pyrene to yield a series of Py-Amylose and Py-PMA constructs, and their ability to form excimer in DMSO was characterized quantitatively by steady-state and time-resolved fluorescence. First, the ratio of the fluorescence intensity of the excimer over that of the monomer, namely the IE/IM ratio, was obtained from the fluorescence spectra. Second, the product ⟨kblob × Nblob⟩ was obtained from the fluorescence blob model (FBM) analysis of the fluorescence decays. Both IE/IM and ⟨kblob × Nblob⟩ yielded similar values when expressed in terms of moles of pyrene per backbone atom for Py-Amylose and Py-PMA. Since IE/IM and ⟨kblob × Nblob⟩ reflect the efficiency of pyrene excimer formation, the similar...  Read more

Assessing Ion–Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations

Journal of Chemical Theory and Computation
AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water–water and water–ion interactions. We find that AMOEBA’s total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on...  Read more

Effective Fully Polarizable QM/MM Approach To Model Vibrational Circular Dichroism Spectra of Systems in Aqueous Solution

Journal of Chemical Theory and Computation
We propose a methodology, based on the combination of classical Molecular Dynamics (MD) simulations with a fully polarizable Quantum Mechanical (QM)/Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) Hamiltonian, to calculate Vibrational Circular Dichroism (VCD) spectra of chiral systems in aqueous solution. Polarization effects are included in the MM force field by exploiting an approach based on Fluctuating Charges (FQ). By performing the MD, the description of the solvating environment is enriched by taking into account the dynamical aspects of the solute–solvent interactions. On the other hand, the QM/FQ/PCM calculation of the VCD spectrum ensures an accurate description of the electronic density of the solute and a proper account for the specific interactions in solution. The application of our approach to (R)-methyloxirane and (l)-alanine in aqueous solution gives calculated spectra in remarkable agreement with their experimental...  Read more

Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations

Biochemistry
Glutamine synthetase is an important enzyme that catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. In mammals, it plays a key role in preventing excitotoxicity in the brain and detoxifying ammonia in the liver. In plants and bacteria, it is fundamental for nitrogen metabolism, being critical for the survival of the organism. In this work, we show how the use of classical molecular dynamics simulations and multiscale quantum mechanics/molecular mechanics simulations allowed us to examine the structural properties and dynamics of human glutamine synthetase (HsGS), as well as the reaction mechanisms involved in the catalytic process with atomic level detail. Our results suggest that glutamine formation proceeds through a two-step mechanism that includes a first step in which the γ-glutamyl phosphate intermediate forms, with a 5 kcal/mol free energy barrier and a −8 kcal/mol reaction free energy, and then a second rate-limiting step involving the...  Read more

Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase

Biochemistry
A 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) electrophilic moiety is post-translationally and autocatalytically generated in homotetrameric histidine ammonia-lyase (HAL) and other enzymes containing the tripeptide Ala-Ser-Gly in a suitably positioned loop. The backbone cyclization step is identical to that taking place during fluorophore formation in green fluorescent protein from the tripeptide Ser-Tyr-Gly, but dehydration, rather than dehydrogenation by molecular oxygen, is the reaction that gives rise to the mature MIO ring system. To gain additional insight into this unique process and shed light on some still unresolved issues, we have made use of extensive molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations implementing the self-consistent charge density functional tight-binding method on a fully solvated tetramer of Pseudomonas putida HAL. Our results strongly support the idea that mechanical compression of the...  Read more

Improving the Force Field Description of Tyrosine–Choline Cation−π Interactions: QM Investigation of Phenol–N(Me)4+ Interactions

Journal of Chemical Theory and Computation
Cation−π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol–tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine–choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly....  Read more

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective

The Journal of Physical Chemistry B
Classical force field (FF) molecular dynamics (MD) simulations of RNA tetranucleotides have substantial problems in reproducing conformer populations indicated by NMR experiments. To provide more information about the possible sources of errors, we performed quantum mechanical (QM, TPSS-D3/def2-TZVP) and molecular mechanics (MM, AMBER parm99bsc0+χOL3) calculations of different r(CCCC), r(GACC), and r(UUUU) conformers obtained from explicit solvent MD simulations. Solvent effects in the static QM and MM calculations were mimicked using implicit solvent models (COSMO and Poisson–Boltzmann, respectively). The comparison of QM and MM geometries and energies revealed that the two methodologies provide qualitatively consistent results in most of the cases. Even though we found some differences, these were insufficient to indicate any systematic corrections of the RNA FF terms that could improve the performance of classical MD in simulating tetranucleotides. On the basis of...  Read more

Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures

Journal of Chemical Information and Modeling
The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an...  Read more

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism

Biochemistry
The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5′-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an SN1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.Read more

Structural Basis of Fullerene Derivatives as Novel Potent Inhibitors of Protein Tyrosine Phosphatase 1B: Insight into the Inhibitory Mechanism through Molecular Modeling Studies

Journal of Chemical Information and Modeling
Protein tyrosine phosphatase 1B (PTP1B) has become an outstanding target for the treatment of diabetes and obesity. Recent research has demonstrated that some fullerene derivatives serve as a new nanoscale-class of potent inhibitors of PTP1B, but the specific mechanism remains unclear. Several molecular modeling methods (molecular docking, molecular dynamics simulations, and molecular mechanics/generalized Born surface area calculations) were integrated to provide insight into the binding mode and inhibitory mechanism of the new class of fullerene inhibitors. The results reveal that PTP1B with an open WPD loop is more susceptible to the combination with the fullerene inhibitor because of their comparable shapes and sizes. When the WPD loop fluctuates to the open conformation, the inhibitor falls into the active pocket and induces conformational rotation of the WPD loop. This rotation is closely related to the reduction of the catalytic activity of PTP1B. In addition, it is suggested...  Read more

Hybridization of a Metal–Organic Framework with a Two-Dimensional Metal Oxide Nanosheet: Optimization of Functionality and Stability

Chemistry of Materials
An effective way to improve the functionalities and stabilities of metal–organic frameworks (MOFs) is developed by employing exfoliated metal oxide 2D nanosheets as matrix for immobilization. Crystal growth of zeolitic imidazolate framework-8 (ZIF-8) nanocrystals on the surface of layered titanate nanosheets yields intimately coupled nanohybrids of ZIF-8-layered titanate. The resulting nanohybrids show much greater surface areas and larger pore volumes than do the pristine ZIF-8, leading to the remarkable improvement of the CO2 adsorption ability of MOF upon hybridization. Of prime importance is that the thermal- and hydrostabilities of ZIF-8 are significantly enhanced by a strong chemical interaction with the robust titanate nanosheet. A strong interfacial interaction between ZIF-8 and the layered titanate is verified by molecular mechanics simulations and spectroscopic analysis. The universal applicability of the present strategy for the coupling of MOFs and metal oxide...  Read more

Achieving Accurate Reduction Potential Predictions for Anthraquinones in Water and Aprotic Solvents: Effects of Inter- and Intramolecular H-Bonding and Ion Pairing

The Journal of Physical Chemistry C
In this combined computational and experimental study, specific chemical interactions affecting the prediction of one-electron and two-electron reduction potentials for anthraquinone derivatives are investigated. For 19 redox reactions in acidic aqueous solution, where AQ is reduced to hydroanthraquinone, density functional theory (DFT) with the polarizable continuum model (PCM) gives a mean absolute deviation (MAD) of 0.037 V for 16 species. DFT(PCM), however, highly overestimates three redox couples with a MAD of 0.194 V, which is almost 5 times that of the remaining 16. These three molecules have ether groups positioned for intramolecular hydrogen bonding that are not balanced with the intermolecular H-bonding of the solvent. This imbalanced description is corrected by quantum mechanics/molecular mechanics (QM/MM) simulations, which include explicit water molecules. The best theoretical estimations result in a good correlation with experiments, V(Theory) =...  Read more

Protonation State of MnFe and FeFe Cofactors in a Ligand-Binding Oxidase Revealed by X-ray Absorption, Emission, and Vibrational Spectroscopy and QM/MM Calculations

Inorganic Chemistry
Enzymes with a dimetal–carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O2) activation. Recently described proteins bind a manganese–iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O2 reduction and an unusual tyrosine–valine ether cross-link formation, as revealed by X-ray crystallography. Advanced X-ray absorption, emission, and vibrational spectroscopy methods and quantum chemical and molecular mechanics calculations provided relative Mn/Fe contents, X-ray photoreduction kinetics, metal–ligand bond lengths, metal–metal distances, metal oxidation states, spin configurations,...  Read more

Reaction Dynamics Following Ionization of Ammonia Dimer Adsorbed on Ice Surface

The Journal of Physical Chemistry A
The ice surface provides an effective two-dimensional reaction field in interstellar space. However, how the ice surface affects the reaction mechanism is still unknown. In the present study, the reaction of an ammonia dimer cation adsorbed both on water ice and cluster surface was theoretically investigated using direct ab initio molecular dynamics (AIMD) combined with our own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method, and the results were compared with reactions in the gas phase and on water clusters. A rapid proton transfer (PT) from NH3+ to NH3 takes place after the ionization and the formation of intermediate complex NH2(NH4+) is found. The reaction rate of PT was significantly affected by the media connecting to the ammonia dimer. The time of PT was calculated to be 50 fs (in the gas phase), 38 fs (on ice), and 28–33 fs (on water clusters). The dissociation of...  Read more

Characterizing the Structures, Spectra, and Energy Landscapes Involved in the Excited-State Proton Transfer Process of Red Fluorescent Protein LSSmKate1

The Journal of Physical Chemistry B
By applying molecular dynamics (MD) simulations and quantum chemical calculations, we have characterized the states and processes involved in the excited-state proton transfer (ESPT) of LSSmKate1. MD simulations identify two stable structures in the electronic ground state of LSSmKate1, one with a protonated chromophore and the other with a deprotonated chromophore, thus leading to two separate low-energy absorption maxima with a large energy spacing, as observed in the calculated and experimentally measured absorption spectra. Proton transfer is induced by electronic excitation. When LSSmKate1 is excited, the electrons in the chromophore are transferred from the phenol ring to the N-acylimine moiety; the acidity of a phenolic hydroxyl group is thus enhanced. The calculated potential energy curves (PECs) exhibit energetic feasibility in the generation of the fluorescent species in LSSmKate1, and the exact agreement between the calculated and experimentally measured values of...  Read more

A Seamless Grid-Based Interface for Mean-Field QM/MM Coupled with Efficient Solvation Free Energy Calculations

Journal of Chemical Theory and Computation
Among various models that incorporate solvation effects into first-principles-based electronic structure theory such as density functional theory (DFT), the average solvent electrostatic potential/molecular dynamics (ASEP/MD) method is particularly advantageous. This method explicitly includes the nature of complicated solvent structures that is absent in implicit solvation methods. Because the ASEP/MD method treats only solvent molecule dynamics, it requires less computational cost than the conventional quantum mechanics/molecular mechanics (QM/MM) approaches. Herein, we present a real-space rectangular grid-based method to implement the mean-field QM/MM idea of ASEP/MD to plane-wave DFT, which is termed “DFT in classical explicit solvents”, or DFT-CES. By employing a three-dimensional real-space grid as a communication medium, we can treat the electrostatic interactions between the DFT solute and the ASEP sampled from MD simulations in a seamless and straightforward manner....  Read more

QM/MM calculations on a newly synthesised oxyluciferin substrate: new insights into the conformational effect

Physical Chemistry Chemical Physics
In this publication we conduct calculations on a newly synthesised red-shifted emitter of luciferin in order to understand what are the main contributions to the colour-shifting emission. Indeed the bioluminescent system, especially from fireflies, is one of the main resources for medical imaging but its efficiency greatly depends on the wavelength of the emission. We performed classical molecular dynamics followed by quantum mechanics/molecular mechanics (QM/MM) calculations, with either density functional theory or multiconfigurational reference second-order perturbation theory on different emitters to obtain bioluminescence emission. We analysed the calculations and investigated the effects which play a non-negligible role in the emission, like the effect of the surroundings or the effect of the conformation of the emitter. Finally, in the absence of crystallographic structures, we proposed the most likely conformation for the emitter in the bioluminescence process.Read more

Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study

The Journal of Physical Chemistry A
We study the linear and nonlinear optical properties of a well-known acid–base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral ⇒ anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral ⇒ anionic and open neutral ⇒...  Read more

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks

Journal of Chemical Theory and Computation
Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three...  Read more