High-level Calculations Research Articles

Physical-model guided self-distillation network for single image dehazing.

Image dehazing, as a key prerequisite of high-level computer vision tasks, has gained extensive attention in recent years. Traditional model-based methods acquire dehazed images via the atmospheric scattering model, which dehazed favorably but often causes artifacts due to the error of parameter estimation. By contrast, recent model-free methods directly restore dehazed images by building an end-to-end network, which achieves better color fidelity. To improve the dehazing effect, we combine the complementary merits of these two categories and propose a physical-model guided self-distillation network for single image dehazing named PMGSDN. First, we propose a novel attention guided feature extraction block (AGFEB) and build a deep feature extraction network by it. Second, we propose three early-exit branches and embed the dark channel prior information to the network to merge the merits of model-based methods and model-free methods, and then we adopt self-distillation to transfer the features from the deeper layers (perform as teacher) to shallow early-exit branches (perform as student) to improve the dehazing effect. For I-HAZE and O-HAZE datasets, better than the other methods, the proposed method achieves the best values of PSNR and SSIM being 17.41dB, 0.813, 18.48dB, and 0.802. Moreover, for real-world images, the proposed method also obtains high quality dehazed results. Experimental results on both synthetic and real-world images demonstrate that the proposed PMGSDN can effectively dehaze images, resulting in dehazed results with clear textures and good color fidelity.

Ion-molecule reactions of mass-selected ions.

Gas-phase reactions of mass-selected ions with neutrals covers a very broad area of fundamental and applied mass spectrometry (MS). Oftentimes, ion-molecule reactions (IMR) can serve as a viable alternative to collision-induced dissociation and other ion dissociation techniques when using tandem MS. This review focuses on the literature pertaining applications of IMR since 2013. During the past decade considerable efforts have been made in analytical applications of IMR, including advances in one of the major techniques for characterization of unsaturated fatty acids and lipids, ozone-induced dissociation, and the development of a new technique for sequencing of large ions, hydrogen atom attachment/abstraction dissociation. Many advances have also been made in identifying gas-phase chemistry specific to a functional group in organic and biological compounds, which are useful in structure elucidation of analytes and differentiation of isomers/isobars. With "soft" ionization techniques like electrospray ionization having become mainstream for quite some time now, the efforts in the area of metal ion catalysis have firmly moved into exploring chemistry of ligated metal complexes in their "natural" oxidation states allowing to model individual steps of mechanisms in homogeneous catalysis, especially in combination with high-level DFT calculations. Finally, IMR continue to contribute to the body of knowledge in the area of chemistry of interstellar processes.

BH4 Ng+ (Ar-Rn): Viable Compounds with a B-Ng Covalent Bond.

In this work, we explore, using high-level calculations, the ability of BH4 + to interact with noble gases. The He system is energetically unstable, while the Ne system could only be observed at cryogenic temperatures. In the case of the Ar, Kr and Xe systems, all are energetically stable, even at room temperature. The different chemical bond descriptors reveal a covalent character between B and the noble gas from Ar to Rn. However, this interaction gradually weakens the multicentric bond between the boron atom and the H2 fragment. Thus, although BH4 Rn+ exhibits a strong covalent bond, it tends to dissociate at room temperature into BH2 Rn+ +H2 .

Transferable Potential Function for Flexible H2O Molecules Based on the Single-Center Multipole Expansion.

A potential function is presented for describing a system of flexible H2O molecules based on the single-center multipole expansion (SCME) of the electrostatic interaction. The model, referred to as SCME/f, includes the variation of the molecular quadrupole moment as well as the dipole moment with changes in bond length and angle so as to reproduce results of high-level electronic structure calculations. The multipole expansion also includes fixed octupole and hexadecapole moments, as well as anisotropic dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole polarizability tensors. The model contains five adjustable parameters related to the repulsive interaction and damping functions in the electrostatic and dispersion interactions. Their values are adjusted to reproduce the lowest energy isomers of small clusters, (H2O)n with n = 2-6, as well as measured properties of the ice Ih crystal. Subsequent calculations of the energy difference between the various isomer configurations of the clusters show that SCME/f gives good agreement with results of electronic structure calculations and represents a significant improvement over the previously presented rigid SCME potential function. Analysis of the vibrational frequencies of the clusters and structural properties of ice Ih crystal show the importance of accurately describing the variation of the quadrupole moment with molecular structures.

Collision-Induced Dissociation of α-Isomaltose and α-Maltose.

Determination of carbohydrate structures remains a considerable challenge. Collision-induced dissociation (CID) tandem mass spectroscopy (MS/MS) is widely used for carbohydrate structure determination. Structural information derived from MS/MS relies on an understanding of the carbohydrate dissociation mechanism. Among various hexose disaccharides, the major dissociation channels (dehydration, glycosidic bond cleavage, and cross-ring dissociation) of 1→2-, 1→3-, and 1→4-linked disaccharide sodium ion adducts can be explained by the dissociation mechanism derived from hexose monosaccharides. However, 1→6-linked disaccharides, which have low branching ratios for dehydration and glycosidic bond cleavage, cannot be explained by the same dissociation mechanism. In this study, we performed high-level quantum chemistry calculations to examine the CID mechanism of the α-isomaltose sodium ion adduct, a 1→6-linked glucose disaccharide. For comparison, we examined the CID dissociation mechanism of the α-maltose sodium ion adduct, a 1→4-linked glucose-disaccharide. Calculations revealed that although α-isomaltose and α-maltose had similar dissociation mechanisms, energy differences between the lowest transition states of various dissociation channels led to different CID fragmentation patterns. The dissociation barriers of dehydration and glycosidic bond cleavage were similar for the two disaccharides, but the cross-ring dissociation, which has the lowest dissociation barrier, exhibited differences in barriers between the disaccharides. The cross-ring dissociation barrier for α-maltose was only slightly lower than those of dehydration and glycosidic bond cleavage. However, the cross-ring dissociation barrier for α-isomaltose was substantially lower than those of dehydration and glycosidic bond cleavage. In addition, most of the α-isomaltose conformers that led to dehydration also led to cross-ring dissociation, resulting in suppression of dehydration by cross-ring dissociation. The findings can explain the low branching ratios for dehydration and glycosidic bond cleavage observed in α-isomaltose CID spectra.

Adsorption energies on transition metal surfaces: towards an accurate and balanced description

Density functional theory predictions of binding energies and reaction barriers provide invaluable data for analyzing chemical transformations in heterogeneous catalysis. For high accuracy, effects of band structure and coverage, as well as the local bond strength in both covalent and non-covalent interactions, must be reliably described and much focus has been put on improving functionals to this end. Here, we show that a correction from higher-level calculations on small metal clusters can be applied to improve periodic band structure adsorption energies and barriers. We benchmark against 38 reliable experimental covalent and non-covalent adsorption energies and five activation barriers with mean absolute errors of 2.2 kcal mol−1, 2.7 kcal mol−1, and 1.1 kcal mol−1, respectively, which are lower than for functionals widely used and tested for surface science evaluations, such as BEEF-vdW and RPBE.

The binding affinity of human pediatric respiratory syncytial virus Phosphoprotein's C-terminal tail to nucleocapsid can be improved by a rationally designed halogen-bonded system

Human respiratory syncytial virus (hRSV) is a common contagious virus that causes infections of pediatric pneumonia and specifically impacts infants and small children. The hRSV phosphoprotein is a key component of the viral RNA polymerase, which can interact with nucleocapsid and other partners through its C-terminal tail (CTT) to promote the formation of viral transcriptase complex, where the Phe241 is a key anchor residue. Based on the crystal template-modeled complex structure of hRSV nucleocapsid with a peptidic segment derived from the phosphoprotein's CTT, we successfully introduced a rationally designed halogen-bonded system to the complex interface by substituting para (p)-position of the side-chain phenyl moiety of CTT Phe241 residue with a halogen atom X (X = F, Cl, Br or I). The halogen-bonded system consists of a halogen bond (X-bond) between nucleocapsid Ser131 residue and CTT Phe241 residue as well as a hydrogen bond (H-bond) between nucleocapsid Ser131 residue and nucleocapsid Glu128 residue; the X-bond and H-bond share a common hydroxyl group of nucleocapsid Ser131 residue. High-level theoretical calculations suggested that bromine Br is the best choice that can render strong potency for the X-bond and can confer high affinity to the nucleocapsid–CTT binding. Affinity analysis revealed that the p-brominated CTT ([p]bCTT) exhibited 6.3-fold affinity improvement relative to its nonhalogenated counterpart. In contrast, the Br-substitutions at ortho (o)- and meta (m)-positions, which resulted in two negative controls of o-brominated [o]bCTT and m-brominated [m]bCTT, respectively, were unable to form effective X-bond with nucleocapsid according to theoretical investigation and did not improve the binding affinity essentially relative to native CTT.

Rate constant determination in the reaction of gold ion with carbonyl using single-atom chemistry in gas phase

The reactions of single gold ion Au+ with CO and H2O molecules in gas phase were studied by experiment and calculation. A reaction tube was connected to the end of the jet to destroy the supersonic state of the molecular beam and enhance the collisions between the laser-sputtered metal ions with gas molecules, so as to ensure the equilibrium reaction conditions. The ionic products were analyzed by a time-of-flight mass spectrometer. The collision temperature in reaction tube was calibrated to 409 K by the reaction of Au+ ion and H2O molecules. The contents of ionic products Au(CO)+ and Au(CO)2+ in the reaction of Au+ with CO molecules were monitored under different concentrations of CO in precursor gas. The combination reaction rate constants of single Au + ion sequentially with two CO molecules were determined to be k1 = 1.1 (2) × 10−12 cm3s−1 and k2 = 4.5 (5) × 10−10 cm3s−1. The geometric structures and binding energies of the ionic products, as well as the pathway and rate constants of the reactions were predicted by a high-level ab initial calculation. The binding mode of Au+ and CO and the formation of molecular orbital were discussed.

Impact of a single water molecule on the atmospheric oxidation of thiophene by hydroperoxyl radical

Water as an important assistant can alter the reactivity of atmospheric species. This project is designed to investigate the impact of a single water molecule on the atmospheric reactions of aromatic compounds that have not been attended to comprehensively. In the first part, the atmospheric oxidation mechanisms of thiophene initiated by hydroperoxyl radical through a multiwell-multichannel potential energy surface were studied to have useful information about the chemistry of the considered reaction. It was verified that for the thiophene plus HO2 reaction, the addition mechanism is dominant the same as other aromatic compounds. Due to the importance of the subject and the presence of water molecules in the atmosphere with a high concentration that we know as relative humidity, and also the lack of insight into the influence of water on the reactions of aromatic compounds with active atmospheric species, herein, the effect of a single water molecule on the addition pathways of the title reaction is evaluated. In another word, this research explores how water can change the occurrence of reactions of aromatic compounds in the atmosphere. For this, the presence of one water molecule is simulated by higher-level calculations (BD(T) method) through the main interactions with the stationary points of the most probable pathways. The results show that the mechanism of the reaction with water is more complicated than the bare reaction due to the formation of the ring-like structures. Also, water molecule decreases the relative energies of all addition pathways. Moreover, atoms in molecule theory (AIM) along with the kinetic study by the transition state (TST) and the Rice–Ramsperger–Kassel–Marcus (RRKM) theories demonstrate that the overall interactions of a path determine how the rate of that path changes. In this regard, our results establish that the interactions of water with HO2 (thiophene) in the initial complex 1WHA (1WTA or 1WTB) are stronger (weaker) than the sum of its interactions in transition states. Also, for the water-assisted pathways, the ratio of the partition function of the transition state to the partition functions of the reactants is similar to the respective bare reaction. Therefore, the reaction rates of the bare pathways are more than the water-assisted paths that include the 1WHA complex and are less than the paths that involve the 1WTA and 1WTB complexes.

Development of a novel ReaxFF reactive potential for organochloride molecules.

This article presents a new reactive potential in the ReaxFF formalism. It aims to include the chlorine element and opens up the fields of use of ReaxFF to the whole class of organochloride compounds including conjugated or aromatic groups. Numerous compounds in this family raise global awareness due to their environmental impact, and such a reactive potential will help investigate their degradation pathways. The new force field, named CHONCl-2022_weak, belongs to the aqueous branch. The force field parameters were fitted against high-level quantum chemistry calculations, including complete active space self-consistent field/NEVPT2 calculations and density functional theory calculations, and their accuracy was evaluated using a validation set. The root means square deviation against quantum mechanics energies is 0.38eV (8.91kcal mol-1). From a structural point of view, the root means square deviation is about 0.06 Å for the bond lengths, 11.86° for the angles, and 4.12° for the dihedral angles. With CHONCl-2022_weak new force field, we successfully investigated the regioselectivity for nucleophilic or electrophilic attacks on polychlorinated biphenyls, which are toxic and permanent pollutants. The rotation barriers along the bond linking the two benzene rings, which is crucial in the toxicity of these compounds, are well reproduced by CHONCl-2022_weak. Then, our new reactive potential is used to investigate the chlorobenzene reactivity in the presence of hydroxyl radicals in atmospheric condition or in aqueous solution. The reaction pathways computed with ReaxFF agree with the quantum mechanics results. We showed that, in the presence of dioxygen molecules, in atmospheric condition, the oxidation of chlorobenzene likely leads to the formation of highly oxygenated compounds after the abstraction of hydrogen radicals. In water, the addition of a hydroxyl radical leads to the formation of chlorophenol or phenol molecules, as already predicted from plasma-induced degradation experiments.

Tightening the Screws: The Importance of Tight d Functions in Coupled-Cluster Calculations up to the CCSDT(Q) Level

It is well established that the basis set convergence of the correlation consistent (cc-pVnZ) basis sets depends on the presence of high-exponent "tight" d functions in the basis set for second-row atoms. The effect has been linked to low-lying 3d virtual orbitals approaching the valence shell. However, since most of this effect is captured at the self-consistent field level, the effect of tight d functions in high-level coupled-cluster calculations has not been extensively studied. Here, we construct an extensive data set of 45 second-row species to examine the effect of tight d functions in CCSD, CCSD(T), CCSDT, and CCSDT(Q) calculations in conjunction with basis sets of up to sextuple-ζ quality. The selected set of molecules covers the gamut from systems where the tight d functions play a relatively minor role (e.g., SiH, SH, SiF, PF3, HOCl, Cl2, and C2Cl2) to challenging systems containing a central second-row atom bonded to many oxygen or fluorine atoms (e.g., PF5, SF6, SO3, ClO3, and HClO4) and systems containing many second-row atoms (e.g., P4, S4, CCl4, and C2Cl6). In conjunction with the cc-pVDZ basis set, we find chemically significant contributions to the total atomization energies (TAEs) of up to ∼2 kcal/mol at the CCSD level, ∼1 kcal/mol at the (T) level, and contributions of up to ∼0.1 kcal/mol for the post-CCSD(T) components. The effects of the tight d functions are diminished with the size of the basis set; however, they are still chemically significant at the CCSD and (T) levels. For example, with the cc-pVTZ basis set, we obtain contributions to the TAEs of up to ∼1.5 and ∼0.3 kcal/mol at the CCSD and (T) levels, respectively, and with the cc-pVQZ basis set, we obtain contributions of up to ∼1.0 and ∼0.2 kcal/mol at the CCSD and (T) levels, respectively. We also find that a simple natural bond orbital population analysis of the 3d orbitals of the second-row atom provides a useful a priori indicator of the magnitude of the effect of tight d functions on post-CCSD(T) contribution to the TAEs in oxide and fluoride systems. These results are particularly important in the context of high-level composite ab initio methods capable of confident benchmark accuracy in thermochemical predictions.

Vibronic coupling in the ground and excited states of the imidazole radical cation.

Vibronic interactions in the ground and two excited states of the imidazole radical cation, X2A″ (π-1), A2A' (nσ-1), and B2A″ (π-1), and the associated nuclear dynamics were studied theoretically. The results were used to interpret the recent photoelectron measurements [M. Patanen et al., J. Chem. Phys. 155, 054304 (2021)]. The present high-level electronic structure calculations employing, in particular, the single, double, and triple excitations and equation-of-motion coupled-cluster method accounting for single and double excitation approaches and complete basis set extrapolation technique for the evaluation of the vertical ionization energies of imidazole indicate that the A 2A' and B 2A″ states are very close in energy and subject to non-adiabatic effects. Our modeling confirms the existence of pronounced vibronic coupling of the A 2A' and B 2A″ states. Moreover, despite the large energy gap of nearly 1.3eV, the ground state X 2A″ is efficiently coupled to the A 2A' state. The modeling was performed within the framework of the three-state linear vibronic coupling problem employing Hamiltonians expressed in a basis of diabatic electronic states and parameters derived from ab initio calculations. The ionization spectrum was computed using the multi-configuration time-dependent Hartree method. The calculated spectrum is in good agreement with the experimental data, allowing for some interpretation of the observed features to be proposed.

Computational NMR of carbohydrates: 1. Glucopyranoses.

A high-level calculation of 1 H and 13 C NMR chemical shifts of α- and β-d-glucopyranoses is carried out at the DFT level with taking into account their conformational composition to reveal the most effective computational protocols. A number of dedicated DFT functionals in combination with Jensen's pcS-n (n = 0-4) family of basis sets were applied to evaluate the most reliable combination. It was found that BHandHLYP/pcS-2 provided the most accurate and reliable computational protocol. Based on the performed calculations, the established computational protocol is generally recommended for the calculation of 1 H and 13 C NMR chemical shifts of a wide series of carbohydrates.

DESIGN OF AN AUTOMATED CONTROL SYSTEM OF A DELTA MANIPULATOR WITH MICROCONTROLLER BASED MACHINE VISION

The design and implementation of a microcontroller vision-based manipulator control system is described. The control system is divided into high and low-level loops. As high-level devices computers or minicomputers have been used when conducting most research. In this work, a microcontroller board has been used as a high-level device due to its mobility and efficiency. A solution to the inverse kinematics task of a delta manipulator is presented in this work which forms the main part of the low-level device algorithm. Sipeed Maixduino and Arduino Mega dev boards have been used to implement the control system. The objects have been classified by YOLO model for the testing purposes of the control system. This has made it possible to measure the average targeting time for the different objects, which is used to test the implemented control system. The empirical data has shown a suboptimal result. The reason for it has been analyzed and addressed through coding a more optimal solution. Potential improvements to the hardware used in the test setup are suggested to benefit future work.

Benchmark Thermochemistry of Polycyclic Aromatic Hydrocarbons.

The DLPNO-CCSD(T1)/CBS method in conjunction with isodesmic-type reactions was used to calculate the enthalpies of formation of 30 polycyclic aromatic hydrocarbons (PAHs). The small reference species with well-determined experimental enthalpies of formation were used in these reactions. From comparison with available experimental data and other recently published high-level quantum chemical calculations, the reference values of the standard enthalpy of formation are recommended for 13 PAHs. The difference between the calculated and experimental values for these compounds does not exceed 2 kJ/mol and their experimental data can be considered as benchmark values for use in calculation of enthalpies of formation of various large PAHs and testing the accuracy of theoretical methods. The use of isodesmic-type reactions involving reference PAHs conserves the structural features of these compounds on both sides of the reaction which leads to a better error compensation. As a result, as shown in the example of coronene, a less-expensive DLPNO-CCSD(T)/CBS method can be used in this case for accurate prediction of enthalpies of formation of large PAHs.

Double Excitation Energies from Quantum Monte Carlo Using State-Specific Energy Optimization.

We show that recently developed quantum Monte Carlo methods, which provide accurate vertical transition energies for single excitations, also successfully treat double excitations. We study the double excitations in medium-sized molecules, some of which are challenging for high-level coupled-cluster calculations to model accurately. Our fixed-node diffusion Monte Carlo excitation energies are in very good agreement with reliable benchmarks, when available, and provide accurate predictions for excitation energies of difficult systems where reference values are lacking.

Spectroscopy and Theoretical Modeling of Tetracene Anion Resonances.

The positions and widths of the optically allowed electronic states of the tetracene radical anion located above the detachment threshold energy (i.e anion resonances) are mapped out using total photodetachment yield spectroscopy of cryogenically cooled ions. The presence of these states is detected via the sharp increase in the photodetachment yield compared to that of the monotonic nonresonant direct photodetachment background. The resolution of the resulting spectrum is limited by the ∼5 cm-1 line width of the tunable laser and thus provides a stringent benchmark for computations of the energies and autodetachment lifetimes of these resonance states. The experimental results are compared to high-level electronic structure computations and line width modeling using the orbital stabilization method. These theoretical results are found to be in near quantitative agreement with the experimental data, highlighting their capability to accurately describe the energies and lifetimes of anion resonances for relatively large molecules.

Ultra-Efficient Optical Gain and Lasing in MDACl2-Doped Perovskite Thin Films

Solution-processed perovskite materials have been enticing candidates for optical gain and lasing media because of their low cost, remarkable color purity, facile bandgap tunability, and high absorption cross-section. However, it is difficult, if not impossible, for them to highly amplify light with stable operations because they experience severe non-radiative emission losses due to their high density of surface and bulk defect centers and irregular composition. Here, we report that incorporating 5% of methylenediammonium dichloride (MDACl2) into mixed perovskite systems leads to a drastic reduction in the density of iodide interstitials and surface recombination losses. Subsequently, we record that MDA-treated, cavity-free thin perovskite films exhibit very photostable and ultra-low threshold amplified spontaneous emission of <6 μJ/cm2, approximately 30 times lower than the untreated films. Moreover, an ultra-high optical gain of 1000 cm–1 is successfully achieved, representing the highest reported gain for cavity-free perovskite films. These results are fully supported by extensive high-level density functional theory calculations and ultrafast transient absorption measurements. These findings will serve as a benchmark for the design and fabrication of low-threshold, high amplification perovskite media for lasers and light emission applications.

Exploring the kinetics and mechanism of C2F5C(O)CF(CF3)2 reaction with hydrogen radical

This work combined high-level quantum chemistry calculations with RRKM/master-equation simulations to gain insight into reactions between C6F12O and hydrogen radical under combustion conditions. The energetics for all stationary points on potential energy surface were determined at CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory. RRKM/master-equation calculations were utilized to simulate the title reaction over a wide range of temperatures and pressures, i.e. 300–3000 K and 0.01–100 atm. Kinetic and mechanistic analyses demonstrate that hydrogen addition to initial adduct C2F5CFCOH(CF3)2 and two dissociations from adduct (CF3)2CFCHOC2F5 to CF3CF2COH + CF3CFCF3 and (CF3)2CFCOH) + CF3CF2 conjointly dominate the overall kinetics over the investigated temperatures and pressures.

Electronic Properties of UN and UN- from Photoelectron Spectroscopy and Correlated Molecular Orbital Theory.

The results of calculations of the properties of the anion UN- including electron detachment are described, which further expand our knowledge of this diatomic molecule. High-level electronic structure calculations were conducted for the UN and UN- diatomic molecules and compared to photoelectron spectroscopy measurements. The low-lying Ω states were obtained using multireference CASPT2 including spin-orbit effects up to ∼20,000 cm-1. At the Feller-Peterson-Dixon (FPD) level, the adiabatic electron affinity (AEA) of UN is estimated to be 1.402 eV and the vertical detachment energy (VDE) is 1.423 eV. The assignment of the UN excited states shows good agreement with the experimental results with a VDE of 1.424 eV. An Ω = 4 ground state was obtained for UN- which is mainly associated with the 3H ΛS state. Thermochemical calculations estimate a bond dissociation energy (BDE) for UN- (U- + N) of 665.9 kJ/mol, ∼15% larger than that of UN and UN+. The NBO analysis reveals U-N triple bonds for the UN, UN-, and UN+ species.