Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment

Small-molecule organic electrode materials on carbon-coated aluminum foil for high-performance sodium-ion batteries

Organic molecular electrode materials are promising candidates in batteries. However, direct application of small molecule materials usually suffers from drastic capacity decay and inefficient utilization of active materials because of their high solubility in organic electrolytes and low electrical conductivity. Herein, a simple strategy is found to address the above issues through coating the small-molecule organic materials on a commercialized carbon-coated aluminum foil (CCAF) as the enhanced electrode. Both the experimental and calculation results confirm that the relatively rough carbon coating on the aluminum foil not only exhibits superior adsorption capacity of small-molecule organic electrode materials with a tight contact interface but also provides continuous electronic conduction channels for the facilitated charge transfer and accelerated reaction kinetics. In addition, the carbon coating also inhibits Al corrosion in electrochemical process. As a result, by using the tetrahydroxy quinone-fused aza-phenazine (THQAP) molecule as an example, the THQAP-CCAF electrode exhibits an excellent rate performance with a high capacity of 220 and 180 mAh g-1 at 0.1 and 2 A/g, respectively, and also a remarkable cyclability with a capacity retention of 77.3% even after 1700 cycles in sodium-ion batteries. These performances are much more superior than that of batteries with the THQAP on bare aluminum foil (THQAP-AF). This work provides a substantial step in the practical application of the small-molecule organic electrode materials for future sustainable batteries.

Time-resolved keto-enol tautomerization of the medicinal pigment curcumin

Curcumin is a medicinal agent that exhibits anti-cancer and anti-Alzheimer's disease properties. It has a keto-enol moiety that gives rise to many of its chemical properties including metal complexation and acid-base equilibria. A previous study has shown that keto-enol tautomerization at this moiety is implicated in the anti-Alzheimer's disease effect of curcumin, highlighting the importance of this process. In this study, tautomerization of curcumin in methanol, acetone and acetonitrile was investigated using time-resolved 1H nuclear magnetic resonance spectroscopy. Curcumin undergoes hydrogen-deuterium exchange with the solvents and the proton resonance peak corresponding to the hydrogen at the α-carbon position (Cα) decays as a function of time, signifying deuteration at this position. Because tautomerization is the rate limiting step in the deuteration of curcumin at the Cα position, the rate of tautomerization is inferred from the rate of deuteration. The rate constant of tautomerization of curcumin shows a temperature dependence and analysis using the Arrhenius equation revealed activation energies (Ea) of tautomerization of (80.1 ± 5.9), (64.1 ± 1.0) and (68.3 ± 5.5) kJ mol-1 in methanol, D2O/acetone and D2O/acetonitrile, respectively. Insight into the role of water in tautomerization of curcumin was further offered by density functional theory studies. The transition state of tautomerization was optimized in the presence of water molecules. The results show a hydrogen-bonded solvent bridge between the diketo moiety and Cα of curcumin. The Ea of tautomerization of curcumin shows a strong dependence on the number of water molecules in the solvent bridge, indicating the critical role played by the solvent bridge in catalyzing tautomerization of curcumin.

A DFTB study on the electronic response of encapsulated DNA nucleobases onto chiral CNTs as a sequencer

Sequencing the DNA nucleobases is essential in the diagnosis and treatment of many diseases related to human genes. In this article, the encapsulation of DNA nucleobases with some of the important synthesized chiral (7, 6), (8, 6), and (10, 8) carbon nanotubes were investigated. The structures were modeled by applying density functional theory based on tight binding method (DFTB) by considering semi-empirical basis sets. Encapsulating DNA nucleobases on the inside of CNTs caused changes in the electronic properties of the selected chiral CNTs. The results confirmed that van der Waals (vdW) interactions, π-orbitals interactions, non-bonded electron pairs, and the presence of high electronegative atoms are the key factors for these changes. The result of electronic parameters showed that among the CNTs, CNT (8, 6) is a suitable choice in sequencing guanine (G) and cytosine (C) DNA nucleobases. However, they are not able to sequence adenine (A) and thymine (T). According to the band gap energy engineering approach and absorption energy, the presence of G and C DNA nucleobases decreased the band gap energy of CNTs. Hence selected CNTs suggested as biosensor substrates for sequencing G and C DNA nucleobases.

Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons

We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.

Green, pH-Sensitive, Highly Stretchable, and Hydrogen Bond-Dominated Ionogel for Wound Healing Activity

Traditional hydrogel dressings generally have poor mechanical properties and stability when subjected to external stress due to the undesirable chain entanglement structure of their single valence bond compositions. Therefore, it is particularly important to develop a type of gel dressing with good mechanical strength, stability, and environment-friendly monitoring. In this work, a transparent, pH-sensitive, highly stretchable, and biocompatible anthocyanidin ionogel dressing was prepared, realizing green and accurate detection. Attributed to the antibacterial activity of the ionic liquid, the biocompatibility of the pectin, and the ability to scavenge free radicals of the anthocyanidin, the ionogel dressing exhibited excellent re-epithelialization in the 14 day wound healing process. Besides, changes in pH values monitoring of the ionogel over 3 days coincided with normal wound exudate. The obtained ionogel also showed good water retention, swelling properties, mechanical stretchability, and 5 week stability, illustrating great potential in wound dressings.

Balance between Physical Interpretability and Energetic Predictability in Widely Used Dispersion-Corrected Density Functionals

We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.

Novel conjugated microporous polymers for efficient tetracycline adsorption: insights from theoretical investigations

This paper presents a detailed theoretical understanding of the noncovalent interactions between antibiotics tetracycline and conjugated microporous polymer (CMP), which is important to understand the recent experimental finding of efficient removal of antibiotics by CMP materials. We show that the co-work of π-π and H-π interactions determines the final equilibrium structures, when a tetracycline molecule spontaneously adsorbs to the surface or within the pores of the CMP network at physisorption distances. The binding energies for tetracycline/CMP systems are calculated to be -0.31 ∼ -1.15 eV, demonstrating the reliability of the adsorption. The electronic structures of CMP nanostructures remain basically undamaged upon the tetracycline adsorption. The replacement of benzothiadiazole unit with S and N heteroatoms to the phenyl moiety in the linker effectively enhanced the molecular polarity of CMP molecule and increases the interaction area between tetracycline and CMP network, consequently enhancing the average binding energies notably. Our calculations provide useful theoretical guidance for design of novel carbon-based porous adsorbents with good adsorption performance to remove residual tetracycline and other antibiotics in water.

Regularized and Opposite Spin-Scaled Functionals from Møller-Plesset Adiabatic Connection─Higher Accuracy at Lower Cost

Noncovalent interactions (NCIs) play a crucial role in biology, chemistry, material science, and everything in between. To improve pure quantum-chemical simulations of NCIs, we propose a methodology for constructing approximate correlation energies by combining an interpolation along the Møller-Plesset adiabatic connection (MP AC) with a regularization and spin-scaling strategy applied to MP2 correlation energies. This combination yields cosκos-SPL2, which exhibits superior accuracy for NCIs compared to any of the individual strategies. With the N4 formal scaling, cosκos-SPL2 is competitive or often outperforms more expensive dispersion-corrected double hybrids for NCIs. The accuracy of cosκos-SPL2 particularly shines for anionic halogen bonded complexes, where it surpasses standard dispersion-corrected DFT by a factor of 3 to 5.

Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules

We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the "Andes" cluster of the Oak Ridge Leadership Computing Facility (OLCF).

Durable organic nonlinear optical membranes for thermotolerant lightings and in vivo bioimaging

Organic nonlinear optical materials have potential in applications such as lightings and bioimaging, but tend to have low photoluminescent quantum yields and are prone to lose the nonlinear optical activity. Herein, we demonstrate to weave large-area, flexible organic nonlinear optical membranes composed of 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium tosylate@cyclodextrin host-guest supramolecular complex. These membranes exhibited a record high photoluminescence quantum yield of 73.5%, and could continuously emit orange luminescence even being heated at 300 °C, thus enabling the fabrication of thermotolerant light-emitting diodes. The nonlinear optical property of these membranes can be well-preserved even in polar environment. The supramolecular assemblies with multiphoton absorption characteristics were used for in vivo real-time imaging of Escherichia coli at 1000 nm excitation. These findings demonstrate to achieve scalable fabrication of organic nonlinear optical materials with high photoluminescence quantum yields, and good stability against thermal stress and polar environment for high-performance, durable optoelectronic devices and humanized multiphoton bio-probes.

An electrochemiluminescence sensor based on CsPbBr3 -zquantum dots and poly (3-thiophene acetic acid) cross-linked nanogold imprinted layer for the determination of benzo(a)pyrene in edible oils

A novel quench molecularly imprinted electrochemiluminescence sensor (MIECLS) based on a covalent organic framework composite (COF-300-Au) with enhanced electrochemiluminescence (ECL) signal from CsPbBr₃ quantum dots and cross-linked 3-thiopheneacetic acid functionalized AuNPs (3-TAA@AuNPs) was developed for the detection of the environmental pollutant benzo(a)pyrene (BaP). A composite material constructed of COF-300-Au with a large specific surface area served as the sensor's support substrate, providing more CsPbBr₃ and imprint recognition sites. Electropolymerization was then employed to form an AuNPs three-dimensional imprinting layer with polythiophene cross-linked using BaP as a template and 3-TAA@AuNPs as a functional monomer. A specific cross-linked imprinting recognition effect was recorded on BaP along with the quenching effect of quinones. The density functional theory (DFT) evaluation of the binding mechanism between 3-TAA@AuNPs and BaP revealed powerful MIECLS toward the detection of BaP at concentrations ranging from 10^-14 to 10^-5M, with a detection limit of as low as 4.1 × 10^-15 M.

Fast and accurate prediction of material properties with three-body tight-binding model for the periodic table

Parametrized tight-binding models fit to first-principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, many previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly 1 000 000 materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low-energy crystal structures and then add them to the fitting data set, iterating until predictions improve. We distribute the materials database and tools developed in this paper publicly.

Structures and stabilities of PAH clusters solvated by water aggregates: The case of the pyrene dimer

Although clusters made of polycyclic aromatic hydrocarbon and water monomers are relevant objects in both atmospheric and astrophysical science, little is known about their energetic and structural properties. In this work, we perform global explorations of the potential energy landscapes of neutral clusters made of two pyrene units and one to ten water molecules using a density-functional-based tight-binding (DFTB) potential followed by local optimizations at the density-functional theory level. We discuss the binding energies with respect to various dissociation channels. It shows that cohesion energies of the water clusters interacting with a pyrene dimer are larger than those of the pure water clusters, reaching for the largest clusters an asymptotic limit similar to that of pure water clusters and that, although the hexamer and octamer can be considered magic numbers for isolated water clusters, it is not the case anymore when they are interacting with a pyrene dimer. Ionization potentials are also computed by making use of the configuration interaction extension of DFTB, and we show that in cations, the charge is mostly carried by the pyrene molecules.

On the recognition of Yersinia protein tyrosine phosphatase by carboxylic acid derivatives

Some members of Yersinia (Y), a genus of bacteria in the family Yersiniaceae, are pathogenic in humans, causing a range of health problems, from gastrointestinal syndromes to the plague. The Y protein tyrosine phosphatase (PTP) YopH is a crucial virulence determinant, considering the vital roles of PTPs in the intracellular signal transduction pathways and cell cycle control. The structural understanding of YopH as a cellular target in pathogenic conditions caused by Y infection is a prerequisite for designing potent and selective YopH inhibitors. Thus, by using molecular docking simulations, the open and closed conformations of the so-called 'WPD loop' (352-Gly-Asn-Trp-Pro-Asp-Gln-Thr-Ala-Val-Ser-361), located nearby the active site (403-Cys-Arg-Ala-Gly-Val-Gly-Arg-Thr-410) in YopH structure, are shown to be relevant for recognition by carboxylic acid derivatives, and the closed conformation is a more preferable receptor in terms of the quantitative correlation with experimental data. In both cases, aurintricarboxylic acid (ATA) has the greatest affinity to YopH. Consequently, a quantum mechanics/molecular mechanics (QM/MM) molecular model is derived to see into the extent of the ATA-induced open-closed conformational change. Active site residues and the WPD loop, as well as ATA are treated using SCC-DFTB-D (QM level), while the rest of the complex is treated using AMBER force field (MM level). The active/inactive functional behavior of YopH is explored by observing the interaction mode of ATA with the wild-type (wt)/Cys403Ser receptor and evaluating the competitive inhibition parameters. Implications of the present study for experimental research are discussed. Communicated by Ramaswamy H. Sarma.

Accurate Hellmann-Feynman forces from density functional calculations with augmented Gaussian basis sets

The Hellmann-Feynman (HF) theorem provides a way to compute forces directly from the electron density, enabling efficient force calculations for large systems through machine learning (ML) models for the electron density. The main issue holding back the general acceptance of the HF approach for atom-centered basis sets is the well-known Pulay force which, if naively discarded, typically constitutes an error upward of 10 eV/Å in forces. In this work, we demonstrate that if a suitably augmented Gaussian basis set is used for density functional calculations, the Pulay force can be suppressed, and HF forces can be computed as accurately as analytical forces with state-of-the-art basis sets, allowing geometry optimization and molecular dynamics to be reliably performed with HF forces. Our results pave a clear path forward for the accurate and efficient simulation of large systems using ML densities and the HF theorem.

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development

This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.

On the inhibition of cytochrome P450 3A4 by structurally diversified flavonoids

Cytochrome P450 3A4 (CYP3A4) is the most versatile enzyme involved in drug metabolism. The time-dependent inhibition of CYP3A4 by acacetin, apigenin, chrysin, and pinocembrin was experimentally detected, but not entirely elaborated so far. Thus, a two-level QM/MM (Quantum Mechanics/Molecular Mechanics) model is developed to yield insights into the receptor-flavonoid recognition at the molecular scale. Active site residues and the flavonoid are modelled using SCC-DFTB-D (QM level), while the rest of the complex is treated using AMBER force field (MM level). QM/MM binding free energies are well correlated with experimental data, indicating the largest inhibitory effect of chrysin on enzyme activity at a submicromolar concentration. Consequently, quercetin (QUE) and flavopiridol (FLP) are observed as representative examples of structurally different flavonoids. The inhibition parameters for QUE and FLP are evaluated using the well-calibrated QM/MM strategy, thereby aiding to quantitatively conceive the functional behavior of the whole family of flavonoids. A kinetic threshold for further assessment of the drug-drug interactions underlying the time-dependent inhibition of CYP3A4 by flavonoids is explored.Communicated by Ramaswamy H. Sarma.

Hydride Relay Exchange Mechanism for the Heterocyclic C-H Arylation of Benzofuran and Benzothiophene Catalyzed by Pd Complexes

The mechanism and regioselectivity of the heterocyclic C-H arylation of benzofuran and benzothiophene catalyzed by Pd(OAc)₂ complexes were investigated using the density functional theory (DFT) method. The Pd(0)L₂(PhI) complex (L = HOAc) is proposed to be the catalytic species. Compared to the traditional Heck-type mechanism, concerted metalation-deprotonation (CMD) mechanism, and electrophilic aromatic substitution (S_EAr) mechanism for the C-H arylation, a new hydride relay exchange mechanism was proposed for the benzoheterocyclic C-H arylation catalyzed by Pd complexes, which consists of two redox processes between Pd(II) and Pd(0) species to complete the regioselective C-H activation. The calculated results indicate that the reaction along the hydride relay exchange mechanism is more favorable than those along other mechanisms, including the traditional Heck-type mechanism and the base-assisted anti-H elimination mechanism. This agrees well with the experimental results. Meanwhile, the origin for the regioselective C-H arylation was unveiled in which the α-C-H arylation products are major for the heterocyclic C-H arylation of benzofuran, but the β-C-H arylation products are major for that of benzothiophene. This study might provide a deep mechanistic understanding on the regioselective C-H activation and arylation of benzoheterocycle compounds catalyzed by transition-metal complexes.

Unusual CO2 Adsorption in ZIF-7: Insight from Raman Spectroscopy and Computational Studies

Here, we use Raman spectroscopy to investigate temperature-dependent changes in the atomic-scale structure of the zeolitic imidazolate framework ZIF-7 in a CO₂ atmosphere and uncover the mechanism of maximal CO₂ adsorption at 206 K. At 301 K, the Raman spectra of ZIF-7 at various CO₂ gas pressures reveal a narrow-pore (np) to large-pore (lp) phase transition commencing at 0.1 bar as a result of adsorption of CO₂, as evident in the appearance of Fermi resonance bands of CO₂ at 1272 and 1376 cm^-1. Moreover, the Raman inactive bending mode of CO₂ becomes active due to geometrical distortion of adsorbed CO₂. It further splits into two peaks due to hydrogen bonding interactions between CO₂ and the benzene ring of the benzimidazole linker ZIF-7, as supported by our computational studies. In addition, the interaction between CO₂ molecules plays a key role. Upon reducing the temperature at 1 bar CO₂ gas pressure, ZIF-7 exhibits softening of the imidazole puckering mode and the Fermi resonance CO₂ band due to interactions between CO₂ and the framework through hydrogen bonding. At 206 K, substantial modification in the lattice mode and disappearance of the Raman inactive CO₂ bending mode confirm the changes in the size of the pore cavity through structural rearrangements of CO₂.

A general tight-binding based energy decomposition analysis scheme for intermolecular interactions in large molecules

In this work, a general tight-binding based energy decomposition analysis (EDA) scheme for intermolecular interactions is proposed. Different from the earlier version [Xu et al., J. Chem. Phys. 154, 194106 (2021)], the current tight-binding based density functional theory (DFTB)-EDA is capable of performing interaction analysis with all the self-consistent charge (SCC) type DFTB methods, including SCC-DFTB2/3 and GFN1/2-xTB, despite their different formulas and parameterization schemes. In DFTB-EDA, the total interaction energy is divided into frozen, polarization, and dispersion terms. The performance of DFTB-EDA with SCC-DFTB2/3 and GFN1/2-xTB for various interaction systems is discussed and assessed.

Density Functional Theory-Based Studies Predict Carbon Nanotubes as Effective Mycolactone Inhibitors

Fullerenes, boron nitride nanotubes (BNNTs), and carbon nanotubes (CNTs) have all been extensively explored for biomedical purposes. This work describes the use of BNNTs and CNTs as mycolactone inhibitors. Density functional theory (DFT) has been used to investigate the chemical properties and interaction mechanisms of mycolactone with armchair BNNTs (5,5) and armchair CNTs (5,5). By examining the optimized structure and interaction energy, the intermolecular interactions between mycolactone and nanotubes were investigated. The findings indicate that mycolactone can be physically adsorbed on armchair CNTs in a stable condition, implying that armchair CNTs can be potential inhibitors of mycolactone. According to DOS plots and HOMO–LUMO orbital studies, the electronic characteristics of pure CNTs are not modified following mycolactone adsorption on the nanotubes. Because of mycolactone’s large π-π interactions with CNTs, the estimated interaction energies indicate that mycolactone adsorption on CNTs is preferable to that on BNNTs. CNTs can be explored as potentially excellent inhibitors of mycolactone toxins in biological systems.

Interaction mechanism of novel fluorescent antifolates targeted with folate receptors α and β via molecular docking and molecular dynamic simulations

Eight novel fluorescent antifolates were designed and docked with folate receptors FRα and FRβ. The structures of the complexes were further calculated by molecular dynamic (MD) simulations. The binding energies were calculated by molecular docking and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) studies. The binding energy differences between FRα and FRβ (|E_bα|-|E_bβ|) values for compounds 3 and 8 were 1.3 and 1.1 kcal/mol calculated by molecular docking, and 13.9 and 10.4 kcal/mol by MM-PBSA simulation, respectively. The results indicated that compounds 3 and 8 may be the best candidates for targeted drug delivery to FRα. The binding structures, interaction residues, negatively charged pocket volume, and surface area were analyzed for all the complexes. We further calculated the root mean square displacement and secondary structural elements of the bound complexes using molecular dynamics simulations. The purpose of this study is to design novel antifolates targeted to FRα and FRβ, and to further distinguish between cancer cells and inflammation.

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

Forces from Stochastic Density Functional Theory under Nonorthogonal Atom-Centered Basis Sets

We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis set representation (Fabian et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci.2019, 9, e1412, 10.1002/wcms.1412) and apply it to the Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the statistical errors in the forces and find that the systematic bias is of the order of 0.065 eV/Å (∼1.2 × 10^–3E_h/a₀) when 120 stochastic orbitals are used, independently of system size. This magnitude of bias is sufficiently small to ensure that the bond lengths estimated by stochastic DFT (within a Langevin molecular dynamics simulation) will deviate by less than 1% from those predicted by a deterministic calculation.

Excited state dynamics of Zn-salophen complexes

Zn-salophen complexes are a promising class of fluorescent chemosensors for nucleotides and nucleic acids. We have investigated, by means of steady state UV-Vis, ultrafast transient absorption, fluorescence emission and time dependent density functional theory (TD-DFT) the behavior of the excited states of a salicylidene tetradentate Schiff base (Sal), its Zn(II) coordination compound (Zn-Sal) and the effect of the interaction between Zn-Sal and adenosine diphosphate (ADP). TD-DFT shows that the deactivation of the excited state of Sal occurs through torsional motion, due to its rotatable bonds and twistable angles. Complexation with Zn(II) causes rigidity so that the geometry changes in the excited states with respect to the ground state structure are minimal. By addition of ADP to a freshly prepared Zn-Sal ethanol solution, a longer relaxation constant, in comparison to Zn-Sal, was measured, indicative of the interaction between Zn-Sal and ADP. After a few days, the Zn-Sal-ADP solution displayed the same static and dynamic behavior of a solution containing only the Sal ligand, demonstrating that the coordination of the ADP anion to Zn(II)leads to the demetallation of the Sal ligand. Fluorescence measurements also revealed an enhanced fluorescence at 375 nm following the addition of ADP to the solution, caused by the presence of 2,3-diamino naphthalene that is formed by demetallation and partial decomposition of the Sal ligand. The efficient fluorescence of this species at 375 nm could be selectively detected and used as a probe for the detection of ADP in solution.

Time-resolved structural analysis of an RNA-cleaving DNA catalyst

The 10-23 DNAzyme is one of the most prominent catalytically active DNA sequences^1,2. Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential². However, the high expectations have not yet been met, a fact that coincides with the lack of high-resolution and time-resolved information about its mode of action³. Here we provide high-resolution NMR characterization of all apparent states of the prototypic 10-23 DNAzyme and present a comprehensive survey of the kinetics and dynamics of its catalytic function. The determined structure and identified metal-ion-binding sites of the precatalytic DNAzyme-RNA complex reveal that the basis of the DNA-mediated catalysis is an interplay among three factors: an unexpected, yet exciting molecular architecture; distinct conformational plasticity; and dynamic modulation by metal ions. We further identify previously hidden rate-limiting transient intermediate states in the DNA-mediated catalytic process via real-time NMR measurements. Using a rationally selected single-atom replacement, we could considerably enhance the performance of the DNAzyme, demonstrating that the acquired knowledge of the molecular structure, its plasticity and the occurrence of long-lived intermediate states constitutes a valuable starting point for the rational design of next-generation DNAzymes.

Conformational Flexibility and Substitution Pattern Lead to Polymorphism of 3-Methyl-2-(phenylamino)benzoic acid

To probe the effect of substitution on the benzoic acid ring on the polymorphism of phenylaminobenzoic acids, five 3-methyl-2-(phenylamino)benzoic acids (MPABAs) were synthesized. A preliminary polymorph screen led to one...

Generation of Quantum Configurational Ensembles Using Approximate Potentials

Conformational analysis is of paramount importance in drug design: it is crucial to determine pharmacological properties, understand molecular recognition processes, and characterize the conformations of ligands when unbound. Molecular Mechanics (MM) simulation methods, such as Monte Carlo (MC) and molecular dynamics (MD), are usually employed to generate ensembles of structures due to their ability to extensively sample the conformational space of molecules. The accuracy of these MM-based schemes strongly depends on the functional form of the force field (FF) and its parametrization, components that often hinder their performance. High-level methods, such as ab initio MD, provide reliable structural information but are still too computationally expensive to allow for extensive sampling. Therefore, to overcome these limitations, we present a multilevel MC method that is capable of generating quantum configurational ensembles while keeping the computational cost at a minimum. We show that FF reparametrization is an efficient route to generate FFs that reproduce QM results more closely, which, in turn, can be used as low-cost models to achieve the gold standard QM accuracy. We demonstrate that the MC acceptance rate is strongly correlated with various phase space overlap measurements and that it constitutes a robust metric to evaluate the similarity between the MM and QM levels of theory. As a more advanced application, we present a self-parametrizing version of the algorithm, which combines sampling and FF parametrization in one scheme, and apply the methodology to generate the QM/MM distribution of a ligand in aqueous solution.

Davis Computational Spectroscopy Workflow-From Structure to Spectra

We describe an automated workflow that connects a series of atomic simulation tools to investigate the relationship between atomic structure, lattice dynamics, materials properties, and inelastic neutron scattering (INS) spectra. Starting from the atomic simulation environment (ASE) as an interface, we demonstrate the use of a selection of calculators, including density functional theory (DFT) and density functional tight binding (DFTB), to optimize the structures and calculate interatomic force constants. We present the use of our workflow to compute the phonon frequencies and eigenvectors, which are required to accurately simulate the INS spectra in crystalline solids like diamond and graphite as well as molecular solids like rubrene. We have also implemented a machine-learning force field based on Chebyshev polynomials called the Chebyshev interaction model for efficient simulation (ChIMES) to improve the accuracy of the DFTB simulations. We then explore the transferability of our DFTB/ChIMES models by comparing simulations derived from different training sets. We show that DFTB/ChIMES demonstrates ∼100× reduction in computational expense while retaining most of the accuracy of DFT as well as yielding high accuracy for different materials outside of our training sets. The DFTB/ChIMES method within the workflow expands the possibilities to use simulations to accurately predict materials properties of increasingly complex structures that would be unfeasible with ab initio methods.

Bispropylurea bridged polysilsesquioxane: A microporous MOF-like material for molecular recognition

Microporous organosilicas assembled from polysilsesquioxane (POSS) building blocks are promising materials that are yet to be explored in-depth. Here, we investigate the processing and molecular structure of bispropylurea bridged POSS (POSS-urea), synthesised through the acidic condensation of 1,3-bis(3-(triethoxysilyl)propyl)urea (BTPU). Experimentally, we show that POSS-urea has excellent functionality for molecular recognition toward acetonitrile with an adsorption level of 74 mmol/g, which compares favourably to MOFs and zeolites, with applications in volatile organic compounds (VOC). The acetonitrile adsorption capacity was 132-fold higher relative to adsorption capacity for toluene, which shows the pores are highly selective towards acetonitrile adsorption due to their size and arrangement. Theoretically, our tight-binding density functional and molecular dynamics calculations demonstrated that this BTPU based POSS is microporous with an irregular placement of the pores. Structural studies confirm maximal pore sizes of ∼1 nm, with POSS cages possessing an approximate edge length of ∼3.16 Å.

Advanced Raman Spectroscopy Detection of Oxidative Damage in Nucleic Acid Bases: Probing Chemical Changes and Intermolecular Interactions in Guanosine at Ultralow Concentration

DNA/RNA synthesis precursors are especially vulnerable to damage induced by reactive oxygen species occurring following oxidative stress. Guanosine triphosphates are the prevalent oxidized nucleotides, which can be misincorporated during replication, leading to mutations and cell death. Here, we present a novel method based on micro-Raman spectroscopy, combined with ab initio calculations, for the identification, detection, and quantification of oxidized nucleotides at low concentration. We also show that the Raman signature in the terahertz spectral range (<100 cm^-1) contains information on the intermolecular assembly of guanine in tetrads, which allows us to further boost the oxidative damage detection limit. Eventually, we provide evidence that similar analyses can be carried out on samples in very small volumes at very low concentrations by exploiting the high sensitivity of surface-enhanced Raman scattering combined with properly designed superhydrophobic substrates. These results pave the way for employing such advanced spectroscopic methods for quantitatively sensing the oxidative damage of nucleotides in the cell.

An Isolable Mononuclear Palladium(I) Amido Complex

Mononuclear Pd(I) species are putative intermediates in Pd-catalyzed reactions, but our knowledge about them is limited due to difficulties in accessing them. Herein, we report the isolation of a Pd(I) amido complex, [(BINAP)Pd(NHAr^Trip)] (BINAP = 2,2'-bis(diphenylphosphino)-1,1'-binaphthalene, Ar^Trip = 2,6-bis(2',4',6'-triisopropylphenyl)phenyl), from the reaction of (BINAP)PdCl₂ with LiNHAr^Trip. This Pd(I) amido species has been characterized by X-ray crystallography, electron paramagnetic resonance, and multiedge Pd X-ray absorption spectroscopy. Theoretical study revealed that, while the three-electron-two-center π-interaction between Pd and N in the Pd(I) complex imposes severe Pauli repulsion in its Pd-N bond, pronounced attractive interligand dispersion force aids its stabilization. In accord with its electronic features, reactions of homolytic Pd-N bond cleavage and deprotonation of primary amines are observed on the Pd(I) amido complex.

Understanding intermolecular interactions of large systems in ground state and excited state by using density functional based tight binding methods

A novel energy decomposition analysis scheme, named DFTB-EDA, is proposed based on the density functional based tight-binding method (DFTB/TD-DFTB), which is a semi-empirical quantum mechanical method based on Kohn-Sham-DFT for large-scale calculations. In DFTB-EDA, the total interaction energy is divided into three terms: frozen density, polarization, and dispersion. Owing to the small cost of DFTB/TD-DFTB, DFTB-EDA is capable of analyzing intermolecular interactions in large molecular systems containing several thousand atoms with high computational efficiency. It can be used not only for ground states but also for excited states. Test calculations, involving the S66 and L7 databases, several large molecules, and non-covalent bonding complexes in their lowest excited states, demonstrate the efficiency, usefulness, and capabilities of DFTB-EDA. Finally, the limits of DFTB-EDA are pointed out.

Hydrogenation of C24 Carbon Clusters: Structural Diversity and Energetic Properties

This work aims at exploring the potential energy surfaces of C24Hn=0,6,12,18,24 using the genetic algorithm in combination with the density functional based tight binding potential. The structural diversity was analyzed using order parameters, in particular the sum of the numbers of 5- and 6-carbon rings R5/6. The most abundant and lowest energy population was designated as the flake population (isomers of variable shapes, large R5/6 values), characterized by an increasing number of spherical isomers when nH/nC increases. Simultaneously, the fraction of the pretzel population (spherical isomers, smaller R5/6 values) increases. The fraction of the cage population (largest R5/6 values) remains extremely minor while the branched population (smallest R5/6 values) remains the highest energy population for all nH/nC ratios. For all C24Hn=0,6,12,18,24 clusters, the evolution of the carbon ring size distribution with energy clearly shows the correlation between the stability and the number of 6-carbon rings. The average values of the ionization potentials of all populations were found to decrease when nH/nC increases, ranging from 7.9 down to 6.4 eV. This trend was correlated to geometric and electronic factors, in particular to carbon hybridization. These results are of astrophysical interest, especially regarding the role of carbon species in the gas ionization.

ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields

The ensemble of structures generated by molecular mechanics (MM) simulations is determined by the functional form of the force field employed and its parameterization. For a given functional form, the quality of the parameterization is crucial and will determine how accurately we can compute observable properties from simulations. While accurate force field parameterizations are available for biomolecules, such as proteins or DNA, the parameterization of new molecules, such as drug candidates, is particularly challenging as these may involve functional groups and interactions for which accurate parameters may not be available. Here, in an effort to address this problem, we present ParaMol, a Python package that has a special focus on the parameterization of bonded and nonbonded terms of druglike molecules by fitting to ab initio data. We demonstrate the software by deriving bonded terms' parameters of three widely known drug molecules, viz. aspirin, caffeine, and a norfloxacin analogue, for which we show that, within the constraints of the functional form, the methodologies implemented in ParaMol are able to derive near-ideal parameters. Additionally, we illustrate the best practices to follow when employing specific parameterization routes. We also determine the sensitivity of different fitting data sets, such as relaxed dihedral scans and configurational ensembles, to the parameterization procedure, and discuss the features of the various weighting methods available to weight configurations. Owing to ParaMol's capabilities, we propose that this software can be introduced as a routine step in the protocol normally employed to parameterize druglike molecules for MM simulations.

The fragment molecular orbital method combined with density-functional tight-binding and periodic boundary conditions

The density-functional tight-binding (DFTB) formulation of the fragment molecular orbital method is combined with periodic boundary conditions. Long-range electrostatics and dispersion are evaluated with the Ewald summation technique. The first analytic derivatives of the energy with respect to atomic coordinates and lattice parameters are formulated. The accuracy of the method is established in comparison to numerical gradients and DFTB without fragmentation. The largest elementary cell in this work has 1631 atoms. The method is applied to elucidate the polarization, charge transfer, and interactions in the solution.

Hydrogen Bond between a Tyrosine Residue and the C-Ring Propionate Has a Direct Influence on Conformation and Absorption of the Bilin Cofactor in Red/Green Cyanobacteriochromes

Cyanobacteriochromes (CBCRs) are photoreceptors of the phytochrome superfamily showing remarkable variability in the wavelengths of the first electronic transition-sometimes denoted as Q band-compared to canonical phytochromes. Both classes carry the same cofactor, a bilin, but the molecular basis for the wide variation of their absorption properties is still a matter of debate. The interaction between the cofactor and the surrounding protein moiety has been proposed as a possible tuning factor. Here, we address the impact of hydrogen-bonding interaction between the covalently bound tetrapyrrole cofactor (phycocyanobilin, PCB) and a conserved tyrosine residue (Y302) in the second GAF (cGMP-specific phosphodiesterase, adenylyl cyclases, and FhlA) domain of the red-/green-switching CBCR AnPixJ (AnPixJg2). In the wild type, AnPixJg2 shows absorption maxima of 648 and 543 nm for the dark-adapted (Pr) and photoproduct (Pg) states, respectively. The Y302F mutation leads to the occurrence of an additional absorption band at 687 nm, which is assigned to a new spectroscopically identified sub-state called P_III. Similar spectral changes result upon mutating the Y302F-homologue in another representative red-/green-switching CBCR, Slr1393g3. Molecular dynamics simulations on the dark-adapted state suggest that the removal of the hydrogen bond leads to an additional PCB sub-state differing in its A- and D-ring geometries. The origin of the Q band satellite in the dark-adapted state is discussed.

Thermochemical stabilities of giant fullerenes using density functional tight binding theory and isodesmic-type reactions

We present a systematic assessment of the density functional tight binding (DFTB) method for calculating heats of formation of fullerenes with isodesmic-type reaction schemes. We show that DFTB3-D/3ob can accurately predict Δ_f H values of the 1812 structural isomers of C₆₀ , reproduce subtle trends in Δ_f H values for 24 isolated pentagon rule (IPR) isomers of C₈₄ , and predict Δ_f H values of giant fullerenes that are in effectively exact agreement with benchmark DSD-PBEP86/def2-QZVPP calculations. For fullerenes up to C₃₂₀ , DFTB Δ_f H values are within 1.0 kJ mol^-1 of DSD-PBEP86/def2-QZVPP values per carbon atom, and on a per carbon atom basis DFTB3-D/3ob yields exactly the same numerical trend of (Δ_f H [per carbon] = 722n^-0.72  + 5.2 kJ mol^-1 ). DFTB3-D/3ob is therefore an accurate replacement for high-level DHDFT and composite thermochemical methods in predicting of thermochemical stabilities of giant fullerenes and analogous nanocarbon architectures.

Simulation and experimental study of fluorescence labeled polyphosphate in microthrix parvicella

To study the binding mechanism of 4',6-diamidino-2-phenylindole (DAPI) and polyphosphate (Poly-P) and find fluorescent dyes which can dye Poly-P better, the interaction model of DAPI and Poly-P was calculated by the self-consistent-charge, density functional tight-binding (SCC-DFTB-D) method, and the binding sites of DAPI and Poly-P were analyzed. Further, Cy3, Rhodamine 6G and Fluorescein, which are structurally similar to DAPI, were selected to analyze their interactions with Poly-P. The binding energies and frontier orbital properties of the complexes were analyzed. These four fluorescent dyes were further used to dye the activated sludge smear and observe the fluorescence property. The Simulation results show that the N-containing indole ring structures in DAPI plays an important role in the interaction with Poly-P; the binding energies for DAPI, Cy3, Rhodamine 6G and Fluorescein with Poly-P are -42.6, -165.4, -34.7 and -28.9 kcal/mol, respectively. The frontier orbital properties for the complexes were studied, which further indicates that the interactions between Cy3, Rhodamine 6G and Poly-P are stronger than that of Fluorescein and Poly-P. The experimental results showed that Cy3 had excellent dyeing effect on Poly-P and could recognize them, while Fluorescein could not dye Poly-P. The experimental results were in good agreement with those predicted by simulation, which verified the correctness of our calculation method and provided a new strategy for finding more reliable, more sensitive and more economical fluorescent dyes capable of dyeing Poly-P.