Q-Chem 2.0: a high-performanceab initio electronic structure program package

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

In Silico Prediction and Molecular Docking of SNPs in NRP1 Gene Associated with SARS-COV-2

Neuropilin-1 (NRP1) which is a main transmembrane cell surface receptor acts as a host cell mediator resulting in increasing the SARS-Cov-2 infectivity and also plays a role in neuronal development, angiogenesis and axonal outgrowth. The goal of this study is to estimate the impact of single nucleotide polymorphisms (SNPs) in the NRP1 gene on the function, structure and stabilization of protein as well as on the miRNA-mRNA binding regions using bioinformatical tools. It is also aimed to investigate the changes caused by SNPs in NRP1 on interactions with drug molecule and spike protein. The missense type of SNPs was analyzed using SIFT, PolyPhen-2, SNAP2, PROVEAN, Mutation Assessor, SNPs&GO, PhD-SNP, I-Mutant 3.0, MUpro, STRING, Project HOPE, ConSurf, and PolymiRTS. Docking analyses were conducted by AutoDock Vina program. As a result, a total of 733 missense SNPs were determined within the NRP1 gene and nine SNPs were specified as damaging to the protein. The modelling results showed that wild and mutant type amino acids had some different properties such as size, charge, and hydrophobicity. Additionally, their three-dimensional structures of protein were utilized for confirmation of these differences. After evaluating the results, nine polymorphisms rs141633354, rs142121081, rs145954532, rs200028992, rs200660300, rs369312020, rs370117610, rs370551432, rs370641686 were determined to be damaging on the structure and function of NRP1 protein and located in conserved regions. The results of molecular docking showed that the binding affinity values are nearly the same for wild-type and mutant structures support that the mutations carried out are not in the focus of the binding site, therefore the ligand does not affect the binding energy. It is expected that the results will be useful for future studies.

Design of Intramolecular Dihedral Angle between Electronic Donor and Acceptor in Thermally Activated Delayed Fluorescence Molecules

In order to improve the exciton utilization efficiency (η_exc) of organic light-emitting materials, we addressed the ideal donor-acceptor dihedral angle (θ_D-A) in the TADF molecule by striking a balance between two photophysical processes. One is the conversion of triplet excitons into singlet excitons, and the other is the radiative process from a low-lying excited state to the ground state. Using a combination of first-principles calculations and molecular dynamics simulations, we investigated the impact of θ_D-A on the splitting energy and spin-orbit coupling between singlet and triplet excitons as well as the transition dipole moment for carbazole benzonitrile (CzBN) derivatives. By comparison with the reverse intersystem crossing rate (k_rISC), fluorescence emission rate (k_r), and η_exc, we proposed a potential highest η_exc (of 94.4%) with the ideal θ_D-A of 77° for blue light CzBN derivatives; the calculated results have a good agreement with experimental measurement. The structure-efficiency physical connection between the molecular structure (θ_D-A) and efficiency provided an ideal parameter for a potential candidate for blue TADF-OLED materials.

Molecular dynamics of fibric acids

¹H- and ¹³C-NMR chemical shifts were measured for four fibric acids (bezafibrate, clofibric acid, fenofibric acid, and gemfibrozil), which are lipid-lowering drugs. Correlation is found with DFT-computed chemical shifts from the conformational analysis. Equilibrium populations of optimized conformers at 298 K are very different when based on computed Gibbs energies rather than on potential energies. This is due to the significant entropic advantages of extended rather than bent conformational shapes. Abundant conformers with intramolecular hydrogen bonding via five-member rings are computed for three fibric acids, but not gemfibrozil, which lacks suitable connectivity of carboxyl and phenoxy groups. Trends in computed atom-positional deviations, molecular volumes, surface areas, and dipole moments among the fibric acids and their constituent conformations indicate that bezafibrate has the greatest hydrophilicity and fenofibric acid has the greatest flexibility. Theoretical and experimental comparison of chemical shifts of standards with sufficient overlap of fragments containing common atoms, groups, and connectivity may provide a reliable minimal set to benchmark and generate leads.

Simulating Electronic Absorption Spectra of Atmospherically Relevant Molecules: A Systematic Assignment for Enhancing Undergraduate STEM Education

Computational and atmospheric chemistry are two important branches of contemporary chemistry. With the present topical nature of climate change and global warming, it is more crucial than ever that students are aware of and exposed to atmospheric chemistry, with an emphasis on how modeling may aid in understanding how atmospherically relevant chemical compounds interact with incoming solar radiation. Nonetheless, computational and atmospheric chemistry are under-represented in most undergraduate chemistry curricula. In this manuscript, we describe a simple and efficient method for simulating the electronic absorption spectral profiles of atmospherically relevant molecules that may be utilized in an undergraduate computer laboratory. The laboratory results give students hands-on experience in computational and atmospheric chemistry, as well as electronic absorption spectroscopy.

Full-dimensional Schrödinger wavefunction calculations using tensors and quantum computers: the Cartesian component-separated approach

Traditional methods in quantum chemistry rely on Hartree-Fock-based Slater-determinant (SD) representations, whose underlying zeroth-order picture assumes separability by particle. Here, we explore a radically different approach, based on separability by Cartesian component, rather than by particle [J. Jerke and B. Poirier, J. Chem. Phys., 2018, 148, 104101]. The approach appears to be very well suited for 3D grid-based methods in quantum chemistry, and thereby also for so-called "first-quantized" quantum computing. We first present an overview of the approach as implemented on classical computers, including numerical results that justify performance claims. In particular, we perform numerical calculations with four explicit electrons that are equivalent to full-CI matrix diagonalization with nearly 10¹⁵ SDs. We then present an implementation for quantum computers for which the number of quantum gates (and to a lesser extent, the number of qubits) can be dramatically reduced, in comparison with other quantum circuitry that has been envisioned for implementing first-quantized "quantum computational chemistry" (QCC).

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

Flyby reaction trajectories: Chemical dynamics under extrinsic force

Dynamic effects are an important determinant of chemical reactivity and selectivity, but the deliberate manipulation of atomic motions during a chemical transformation is not straightforward. Here, we demonstrate that extrinsic force exerted upon cyclobutanes by stretching pendant polymer chains influences product selectivity through force-imparted nonstatistical dynamic effects on the stepwise ring-opening reaction. The high product stereoselectivity is quantified by carbon-13 labeling and shown to depend on external force, reactant stereochemistry, and intermediate stability. Computational modeling and simulations show that, besides altering energy barriers, the mechanical force activates reactive intramolecular motions nonstatistically, setting up "flyby trajectories" that advance directly to product without isomerization excursions. A mechanistic model incorporating nonstatistical dynamic effects accounts for isomer-dependent mechanochemical stereoselectivity.

Molecular modeling approaches to address drug-metabolizing enzymes (DMEs) mediated chemoresistance: a review

Resistance against clinically approved anticancer drugs is the main roadblock in cancer treatment. Drug metabolizing enzymes (DMEs) that are capable of metabolizing a variety of xenobiotic get overexpressed in malignant cells, therefore, catalyzing drug inactivation. As evident from the literature reports, the levels of DMEs increase in cancer cells that ultimately lead to drug inactivation followed by drug resistance. To puzzle out this issue, several strategies inclusive of analog designing, prodrug designing, and inhibitor designing have been forged. On that front, the implementation of computational tools can be considered a fascinating approach to address the problem of chemoresistance. Various research groups have adopted different molecular modeling tools for the investigation of DMEs mediated toxicity problems. However, the utilization of these in-silico tools in maneuvering the DME mediated chemoresistance is least considered and yet to be explored. These tools can be employed in the designing of such chemotherapeutic agents that are devoid of the resistance problem. The current review canvasses various molecular modeling approaches that can be implemented to address this issue. Special focus was laid on the development of specific inhibitors of DMEs. Additionally, the strategies to bypass the DMEs mediated drug metabolism were also contemplated in this report that includes analogs and pro-drugs designing. Different strategies discussed in the review will be beneficial in designing novel chemotherapeutic agents that depreciate the resistance problem.

Effect of molecular constitution and conformation on positron binding and annihilation in alkanes

The model-potential approach previously developed by the authors to study positron interactions with molecules is used to calculate the positron binding energy for n-alkanes (C_nH_2n+2) and the corresponding cycloalkanes (C_nH_2n). For n-alkanes, the dependence of the binding energy on the conformation of the molecule is investigated, with more compact structures showing greater binding energies. As a result, thermally averaged binding energies for larger alkanes (n ≳ 9) show a strong temperature dependence in the range of 100 K-600 K. This suggests that positron resonant annihilation can be used as a probe of rotational (trans-gauche) isomerization of n-alkanes. In particular, the presence of different conformers leads to shifts and broadening of vibrational Feshbach resonances in the annihilation rate, as observed with a trap-based low-energy positron beam.

Evaluating Simple Ab Initio Models of the Hydrated Electron: The Role of Dynamical Fluctuations

Despite its importance in electron transfer reactions and radiation chemistry, there has been disagreement over the fundamental nature of the hydrated electron, such as whether or not it resides in a cavity. Mixed quantum/classical simulations of the hydrated electron give different structures depending on the pseudopotential employed, and ab initio models of computational necessity use small numbers of water molecules and/or provide insufficient statistics to compare to experimental observables. A few years ago, Kumar et al. (J. Phys. Chem. A 2015, 119, 9148) proposed a minimalist ab initio model of the hydrated electron with only a small number of explicitly treated water molecules plus a polarizable continuum model (PCM). They found that the optimized geometry had four waters arranged tetrahedrally around a central cavity, and that the calculated vertical detachment energy and radius of gyration agreed well with experiment, results that were largely independent of the level of theory employed. The model, however, is based on a fixed structure at 0 K and does not explicitly incorporate entropic contributions or the thermal fluctuations that should be associated with the room-temperature hydrated electron. Thus, in this paper, we extend the model of Kumar et al. by running Born-Oppenheimer molecular dynamics (BOMD) of a small number of water molecules with an excess electron plus PCM at room temperature. We find that when thermal fluctuations are introduced, the level of theory chosen becomes critical enough when only four waters are used that one of the waters dissociates from the cluster with certain density functionals. Moreover, even with an optimally tuned range-separated hybrid functional, at room temperature the tetrahedral orientation of the 0 K first-shell waters is entirely lost and the central cavity collapses, a process driven by the fact that the explicit water molecules prefer to make H-bonds with each other more than with the excess electron. The resulting average structure is quite similar to that produced by a noncavity mixed quantum/classical model, so that the minimalist 4-water BOMD models suffer from problems similar to those of noncavity models, such as predicting the wrong sign of the hydrated electron's molar solvation volume. We also performed BOMD with 16 explicit water molecules plus an extra electron and PCM. We find that the inclusion of an entire second solvation shell of explicit water leads to little change in the outcome from when only four waters were used. In fact, the 16-water simulations behave much like those of water cluster anions, in which the electron localizes at the cluster surface, showing that PCM is not acceptable for use in minimalist models to describe the behavior of the bulk hydrated electron. For both the 4- and 16-water models, we investigate how the introduction of thermal motions alters the predicted absorption spectrum, vertical detachment energy, and resonance Raman spectrum of the simulated hydrated electron. We also present a set of structural criteria that can be used to numerically determine how cavity-like (or not) a particular hydrated electron model is. All of the results emphasize that the hydrated electron is a statistical object whose properties are inadequately captured using only a small number of explicit waters, and that a proper treatment of thermal fluctuations is critical to understanding the hydrated electron's chemical and physical behavior.

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field

The CHARMM Drude-2013 polarizable force field (FF) was developed to include the explicit treatment of induced electronic polarizability, resulting in a more accurate description of the electrostatic interactions in molecular dynamics (MD) simulations. While the Drude-2013 protein FF has shown success in improving the folding properties of α-helical peptides and to reproduce experimental observables in simulations up to 1 μs, some limitations were noted regarding the stability of β-sheet structures in simulations longer than 100 ns as well as larger deviations from crystal structures in simulations of a number of proteins compared to the additive CHARMM36 protein FF. The origin of the instability has been identified and appears to be primarily due to overestimated atomic polarizabilities and induced dipole-dipole interactions on the Cβ, Cγ, and Cδ side chain atoms. To resolve this and other issues, a number of aspects of the model were revisited, resulting in Drude-2019 protein FF. Backbone parameters were optimized targeting the conformational properties of the (Ala)5 peptide in solution along with gas phase properties of the alanine dipeptide. Dipeptides that contain N-acetylated and N'-methylamidated termini, excluding Gly, Pro, and Ala, were used as models to optimize the atomic polarizabilities and Thole screening factors on selected Cβ, Cγ, and Cδ carbons by targeting quantum mechanical (QM) dipole moments and molecular polarizabilities. In addition, to obtain better conformational properties, side chain χ1 and χ2 dihedral parameters were optimized targeting QM data for the respective side chain dipeptide conformations as well as Protein Data Bank survey data based on the χ1, χ2 sampling from Hamiltonian replica-exchange MD simulations of (Ala)4-X-(Ala)4 in solution, where X is the amino acid of interest. Further improvements include optimizing nonbonded interactions between charged residues to reproduce QM interaction energies of the charged-protein model compounds and experimental osmotic pressures. Validation of the optimized Drude protein FF includes MD simulations of a collection of peptides and proteins including β-sheet structures, as well as transmembrane ion channels. Results showed that the updated Drude-2019 protein FF yields smaller overall root-mean-square differences of proteins as compared to the additive CHARMM36m and Drude-2013 FFs as well as similar or improved agreement with experimental NMR properties, allowing for long time scale simulation studies of proteins and more complex biomolecular systems in conjunction with the remainder of the Drude polarizable FF.

Synthesis and Electrocatalytic HER Studies of Carbene-Ligated Cu3-xP Nanocrystals

N-heterocyclic carbenes (NHCs) are an important class of ligands capable of making strong carbon-metal bonds. Recently, there has been a growing interest in the study of carbene-ligated nanocrystals, primarily coinage metal nanocrystals, which have found application as catalysts for numerous reactions. The general ability of NHC ligands to positively affect the catalytic properties of other types of nanocrystal catalysts remains unknown. Herein, we present the first carbene-stabilized Cu_3-xP nanocrystals. Inquiries into the mechanism of formation of NHC-ligated Cu_3-xP nanocrystals suggest that crystalline Cu_3-xP forms directly as a result of a high-temperature metathesis reaction between a tris(trimethylsilyl)phosphine precursor and an NHC-CuBr precursor, the latter of which behaves as a source of both the carbene ligand and Cu⁺. To study the effect of the NHC surface ligands on the catalytic performance, we tested the electrocatalytic hydrogen evolving ability of the NHC-ligated Cu_3-xP nanocrystals and found that they possess superior activity to analogous oleylamine-ligated Cu_3-xP nanocrystals. Density functional theory calculations suggest that the NHC ligands minimize unfavorable electrostatic interactions between the copper phosphide surface and H⁺ during the first step of the hydrogen evolution reaction, which contributes to the superior performance of NHC-ligated Cu_3-xP catalysts as compared to oleylamine-ligated Cu_3-xP catalysts.

Mitochondria-Targeted New Blue Light-Emitting Fluorescent Molecular Probe

Discovery of a nontoxic fluorescent molecular probe to "light up" specific cellular organelles is extremely essential to understand dynamics of intracellular components. Here, we report a new nontoxic mitochondria-targeted linear bithiazole compound, containing trifluoroacetyl terminal groups, which emits intense blue fluorescence and stained mitochondria of various cells. Interestingly, the power of fluorescence is completely off when the bithiazole unit is stapled by a carbonyl bridge.

Power of Tyrosine Assembly in Microtubule Stabilization and Neuroprotection Fueled by Phenol Appendages

Microtubules play a crucial role in maintenance of structure, function, axonal extensions, cargo transport, and polarity of neurons. During neurodegenerative diseases, microtubule structure and function get severely damaged due to destabilization of its major structural proteins. Therefore, design and development of molecules that stabilize these microtubule networks have always been an important strategy for development of potential neurotherapeutic candidates. Toward this venture, we designed and developed a tyrosine rich trisubstituted triazine molecule (TY3) that stabilizes microtubules through close interaction with the taxol binding site. Detailed structural investigations revealed that the phenolic protons are the key interacting partners of tubulin. Interestingly, we found that this molecule is noncytotoxic in PC12 derived neurons, stabilizes microtubules against nocodazole induced depolymerization, and increases expression of acetylated tubulin (Ac-K40), an important marker of tubulin stability. Further, results show that TY3 significantly induces neurite sprouting as compared to the untreated control as well as the two other analogues (TS3 and TF3). It also possesses anti-Aβ fibrillation properties as confirmed by ThT assay, which leads to its neuroprotective effect against amyloidogenic induced toxicity caused through nerve growth factor (NGF) deprivation in PC12 derived neurons. Remarkably, our results reveal that it reduces the expression of TrkA (pY490) associated with NGF deprived amyloidogenesis, which further proves that it is a potent amyloid β inhibitor. Moreover, it promoted the health of the rat primary cortical neurons through higher expression of key neuronal markers such as MAP2 and Tuj1. Finally, we observed that it has good serum stability and has the ability to cross the blood-brain barrier (BBB). Overall, our work indicates the importance of phenolic -OH in promoting neuroprotection and its importance could be implemented in the development of future neurotherapeutics.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Molden 2.0: quantum chemistry meets proteins

Since the first distribution of Molden in 1995 and the publication of the first article about this software in 2000 work on Molden has continued relentlessly. A few of the many improved or fully novel features such as improved and broadened support for quantum chemistry calculations, preparation of ligands for use in drug design related softwares, and working with proteins for the purpose of ligand docking.

Participation of C-H Protons in the Dissociation of a Proton Deficient Dipeptide

The dissociation of anionic dipeptides Phe*Gly and GlyPhe*, where Phe* refers to sulfonated phenyl alanine, has been investigated by using ion trap mass spectrometry. The dipeptides undergo collision-induced dissociation (CID) to give the same products, indicating that they rearrange to a common structure before dissociation. The rearrangement does not occur with the dipeptide methyl esters. The structures of the b₂ ions were investigated to determine the effect that having a remote, anionic site has on product formation. Comparison with the CID spectra for authentic structures shows that the b₂ ion obtained from GlyPhe* has predominantly a diketopiperazine structure. The CID spectra for the Phe*Gly b₂ ion and the authentic oxazolone are similar, but differences in intensity suggest a two-component mixture. Isotopic labeling studies are consistent with the formation of two products, with one resulting from loss of a non-mobile proton on the Gly α-carbon. The results are attributed to the formation of an oxazole and oxazolone enol product. Electronic structure calculations predict that the enol structure of the Phe*Gly b₂ ion is lower in energy than the keto version due to intramolecular hydrogen bonding with the sulfonate group. Graphical Abstract ᅟ.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

UPLC-QTOFMS(E)-Guided Dereplication of the Endangered Chinese Species Garcinia paucinervis to Identify Additional Benzophenone Derivatives

A number of Garcinia species accumulate benzophenone derivatives that may be useful for the treatment of breast cancer. The dereplication of new benzophenone derivatives from Garcinia species is challenging due to the occurrence of multiple isomers and the known compounds found in their extracts. In the current study, a strategy is described using the UPLC-QTOFMS(E) technique to identify tentatively the known and uncharacterized benzophenones of interest based upon the characteristic fragmentation ions. Several UPLC-QTOFMS peaks (a-ee) appeared to contain benzophenone derivatives, and 12 of these peaks contained compounds with MS ionization profiles not consistent with previously identified compounds from the seeds of Garcinia paucinervis, an endangered Chinese species. The targeted isolation of unidentified compounds of interest afforded five new benzophenones, paucinones E-I (1-5), which were determined by MS and NMR analysis and ECD spectroscopy. These compounds were evaluated for cytotoxicity against three breast cancer cell lines inclusive of MDA-MB-231, SKBR3, and MCF-7. These results indicate that the UPLC-QTOFMS(E)-guided isolation procedure is an efficient strategy for isolating new benzophenones from Garcinia species.

Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces

In just over a decade since its discovery, research on graphene has exploded due to a number of potential applications in electronics, materials, and medicine. In its water-soluble form of graphene oxide, the material has shown promise as a biosensor due to its preferential absorption of single-stranded polynucleotides and fluorescence quenching properties. The rational design of these biosensors, however, requires an improved understanding of the binding thermodynamics and ultimately a predictive model of sequence-specific binding. Toward these goals, here we directly measured the binding of nucleosides and oligonucleotides to graphene oxide nanoparticles using isothermal titration calorimetry and used the results to develop molecular models of graphene-nucleic acid interactions. We found individual nucleosides binding KD values lie in the submillimolar range with binding order of rG < rA < rC < dT < rU, while 5mer and 15mer oligonucleotides had markedly higher binding affinities in the range of micromolar and submicromolar KD values, respectively. The molecular models developed here are calibrated to quantitatively reproduce the above-mentioned experimental results. For oligonucleotides, our model predicts complex binding features such as double-stacked bases and a decrease in the fraction of graphene stacked bases with increasing oligonucleotide length until plateauing beyond ∼10-15 nucleotides. These experimental and computational results set the platform for informed design of graphene-based biosensors, further increasing their potential and application.

Contribution of Electrostatics to the Kinetics of Electron Transfer from NADH-Cytochrome b5 Reductase to Fe(III)-Cytochrome b5

Brownian dynamics (BD) simulations provide here a theoretical atomic-level treatment of the reduction of human ferric cytochrome b5 (cyt b5) by NADH-cytochrome b5 reductaste (cyt b5r) and several of its mutants. BD is used to calculate the second-order rate constant of electron transfer (ET) between the proteins for direct correlation with experiments. Interestingly, the inclusion of electrostatic forces dramatically increases the reaction rate of the native proteins despite the overall negative charge of both proteins. The role played by electrostatic charge distribution in stabilizing the ET complexes and the role of mutations of several amino acid residues in stabilizing or destabilizing the complexes are analyzed. The complex with the shortest ET reaction distance (d = 6.58 Å) from rigid body BD is further subjected to 1 ns of molecular dynamics (MD) in a periodic box of TIP3P water to produce a more stable complex allowed by flexibility and with a shorter average reaction distance d = 6.02 Å. We predict a docking model in which the following ion-ion interactions are dominant (cyt b5r/cyt b5): Lys162-Heme O1D/Lys163-Asp64/Arg91-Heme O1A/Lys125-Asp70.

VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems

Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.

Development of the ReaxFFCBN reactive force field for the improved design of liquid CBN hydrogen storage materials

ReaxFF_CBN can be used for the improved design of liquid carbon–boron–nitrogen hydrogen-storage materials.

Bodipy recognizes polyaromatic hydrocarbons via C–H⋯F type weak H-bonding

Polycyclic aromatic hydrocarbons (PAHs) demonstrated unusual weak C–H⋯F type H-bonding interaction with meso-substituted Bodipy dyes (1–3) in ethanol medium.

Size-dependent properties of transition metal clusters: from molecules to crystals and surfaces--computational studies with the program ParaGauss

In the so-called scalable regime the size-dependent behavior of the physical and chemical properties of transition metal clusters is described by scaling relationships. For most quantities this scalable regime is reached for cluster sizes between a few tens and a few hundreds of atoms, hence for systems for which an accurate treatment by density functional theory is still feasible. Thus, by invoking scaling relations one is able to obtain properties of very large nanoparticles and even the bulk limit from the results of a series of smaller cluster models. In this invited review we illustrate this strategy by exploiting results from computational studies that mostly were carried out with the density functional theory software ParaGauss. We address mainly the size-dependent behavior of the properties of transition metal clusters. To this end, we first present benchmark studies probing various approximations that are used in such density functional calculations. Subsequently we show how physical insight may be gained by exploring less understood types of systems. These applications range from bare clusters to nanoislands and nanoalloys to adsorption complexes.

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology

Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations.

Mechanisms of reactions of sulfur hydride hydroxide: tautomerism, condensations, and C-sulfenylation and O-sulfenylation of 2,4-pentanedione

The conformations, equilibrium structures, hydrogen bonds, and non-covalent interactions involved in the mechanisms of tautomerization, condensations, and C-sulfenylation and O-sulfenylation of 2,4-pentanedione by sulfur hydride hydroxide (hydrogen thioperoxide, oxadisulfane, H-SOH) have been studied using BD(T), CCSD(T), and QCISD(T) with the cc-pVTZ basis set and using B3LYP, B3PW91, CAM-B3LYP, PBE1PBE, PBEh1PBE, LC-ωPBE, M06-2X, and ωB97XD with the 6-311+G(d,p) basis set. All levels of theory predict the sulfenyl (H-SOH) tautomer of hydrogen thioperoxide to be lower in energy than the sulfinyl (H2S═O) tautomer. Four reasonable mechanisms were considered for the tautomerization of the sulfenyl tautomer of hydrogen thioperoxide to the sulfinyl tautomer: a cyclic three-membered water-free transition state (TS, CCSD(T) activation energy barrier E(⧧) = 65.1 kcal/mol), a cyclic five-membered transition state with one water molecule (TSH2O, E(⧧) = 31.1 kcal/mol), a cyclic seven-membered transition state with two water molecules (TS2H2O, E(⧧) = 14.5 kcal/mol), and a cyclic nine-membered transition state with three water molecules (TS3H2O, E(⧧) = 5.6 kcal/mol). The mechanisms involve hydrogen-bonded reactant complexes and hydrogen-bonded product complexes. The CCSD(T)-predicted energy barriers for the condensation of hydrogen thioperoxide to form thiosulfinic acid through transition states with zero, one, and two waters are E(⧧) = 42.0, 18.3, and 0 kcal/mol, respectively. Mixed condensation reactions are predicted to afford organosulfur products and compounds containing sulfur-selenium bonds. Hydrogen thioperoxide is predicted to add to 2,4-pentanedione to form C-sulfenylated (sulfide, thioether) and O-sulfenylated (sulfenate ester) products. Similar mechanistic trends and reaction pathways are observed in the tautomerism, condensations, and C-sulfenylation and O-sulfenylation reactions of hydrogen thioperoxide. The water molecules set up proton relay networks (bridges) that reduce ring strain, generate favorable conformations for reactivity, lower energy barriers, and increase the numbers of stabilizing hydrogen bonds and nonbonding interactions.

Quinone–Bodipy H-bonding interaction over π-stacking in toluene

Quinone type compounds (o-chloranil, p-chloranil and DDQ) demonstrate excellent H-bonding interactions with a meso-phenol Bodipy dye (1) in both ground and excited state in a non-polar toluene medium.

Isochromenones, isobenzofuranone, and tetrahydronaphthalenes produced by Paraphoma radicina, a fungus isolated from a freshwater habitat

Six isochromenones (1-6), clearanols F (5) and G (6), one isobenzofuranone (7), and two tetrahydronaphthalene derivatives (8 and radinaphthalenone (9)), were isolated and identified from a culture of the fungus Paraphoma radicina, which was isolated from submerged wood in a freshwater lake. Compounds 5, 6 and 9 were previously unknown. The structures were elucidated using a set of spectroscopic and spectrometric techniques; the absolute configurations of compounds 5 and 6 were determined by comparison of their experimental ECD measurements with values predicted by TDDFT calculations. Compounds 1-9 were evaluated for antimicrobial activity against an array of bacteria and fungi. The inhibitory activity of compound 4 against Staphylococcus aureus biofilm formation was evaluated.