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The paper presents a quantum chemical approach for assessment of the thermodynamic parameters of association for alkanes CnH2n+2 (n = 6–14) and polyaromatic hydrocarbons (PAH) of the coronene series as model structures of the graphene surface within the framework of semiempirical methods. The enthalpy, entropy and Gibbs energy of formation and binding for alkanes with PAH were calculated using the PM3 and PM6-DH2 methods. It is shown that an adequate description of the interactions in the regarded complexes requires the use of PM6-DH2 method, since it contains corrections for dispersion interactions and hydrogen bonds. The parallel orientation of the alkane molecule relative to the coronene plane is proved to be more energetically preferable than perpendicular one, which is consistent with experimental data.Intermolecular C–H/π interactions are revealed to be crucial in the 2D film formation of alkanes on graphene/graphite. While interactions between alkane molecules make a destabilizing contribution due to the implementation of energetically unfavorable types of intermolecular CH/HC interactions. This stipulates a threshold chain length of alkanes capable of film formation on the graphene/graphite surface at standard temperature: 14 and 19 carbon atoms for parallel and perpendicular oriented alkanes, respectively. The obtained threshold values of the alkane chain length, as well as the geometric parameters of their orientation in 2D monolayers on the graphene/graphite surface are consistent with available experimental data.

The semiempirical GFNn‐xTB (n=1,2) tight‐binding methods are extended with a spin‐dependent energy term (spin‐polarization), enabling the fast and efficient screening of different spin states for transition metal complexes. While GFNn‐xTB methods inherently can not differentiate properly between high‐spin (HS) and low‐spin (LS) states, this shortcoming is corrected with the presented methods termed spGFNn‐xTB. The performance of spGFNn‐xTB methods for spin state energy splittings is evaluated on a newly compiled benchmark set of 90 complexes (27 HS and 63 LS complexes) containing 3d, 4d, and 5d transition metals (termed TM90S) employing DFT references at the TPSSh‐D4/def2‐QZVPP level of theory. The challenging TM90S set contains complexes with charges between −4 and +3, spin multiplicities between 1 and 6, and spin‐splitting energies that range from −47.8 to 146.6 kcal/mol with a mean average of 32.2 kcal/mol. On this set the (sp)GFNn‐xTB methods, the PM6‐D3H4 method, and the PM7 method are evaluated with spGFN1‐xTB yielding the lowest MAD of 19.6 kcal/mol followed by spGFN2‐xTB with 24.8 kcal/mol. While for the 4d and 5d subsets small or no improvements are observed with spin‐polarization, large improvements are obtained for the 3d subset with spGFN1‐xTB yielding the smallest MAD of 14.2 kcal/mol followed by spGFN2‐xTB with 17.9 kcal/mol and PM6‐D3H4 with 28.4 kcal/mol. The correct sign of the spin state splittings is obtained with spGFN2‐xTB in 89% of all cases closely followed by spGFN1‐xTB with 88%. On the full set, a pure semiempirical vertical spGFN2‐xTB//GFN2‐xTB‐based workflow for screening purposes yields a slightly better MAD of 22.2 kcal/mol due to error compensation, while being qualitative correct for one additional case. In combination with their low computational cost (scanning spin states in seconds), the spGFNn‐xTB methods represent robust tools for pre‐screening steps of spin state calculations and high‐throughput workflows. [ABSTRACT FROM AUTHOR]

In this research, the synthesis, photochemistry, and computational study of new cis- and trans-isomers of amino-thienostilbenes is performed to test the efficiency of their production and acid resistance, and to investigate their electronic structure, photoreactivity, photophysical characteristics, and potential biological activity. The electronic structure and conformations of synthesized thienostilbene amines and their photocyclization products are examined computationally, along with molecular modeling of amines possessing two thiophene rings that showed inhibitory potential toward cholinesterases. New amino-styryl thiophenes, with favorable photophysical properties and proven acid resistance, represent model compounds for their water-soluble ammonium salts as potential styryl optical dyes. The comparison with organic dyes possessing a trans-aminostilbene subunit as the scaffold shows that the newly synthesized trans-aminostilbenes have very similar absorbance wavelengths. Furthermore, their functionalized cis-isomers and photocyclization products are good candidates for cholinesterase inhibitors because of the structural similarity of the molecular skeleton to some already proven bioactive derivatives. [ABSTRACT FROM AUTHOR]

Performance of contemporary tight‐binding semiempirical GFNn‐xTB methods for the conformational energies of singly charged sodium clusters Na+(S)n (n = 4–8) with 3 protic and 8 aprotic solvents is examined against the reference RI‐MP2/CBS method. The median Pearson correlation coefficients of ρ = 0.84 (GFN2‐xTB) and ρ = 0.82 (GFN1‐xTB) do not give the clear preference to any tested approach. GFN1‐xTB method demonstrates more stable performance than its GFN2‐xTB successor with the average mean absolute errors (MAEs)/mean signed errors (MSEs) of 1.2/0.2 and 2.3/1.6 kcal mol−1, respectively. Conformational energies produced by the computationally efficient DFT functional PBE and double‐ζ basis set complemented with –D3(BJ) dispersion correction are suitable for the preliminary sampling (median ρ = 0.93), but should be used with a caution for the calculations of the average ensemble properties (MAE/MSE = 1.7/1.1 kcal mol−1). Higher‐ranking PBE0‐D3(BJ) and ωB97M‐V with triple‐ζ basis sets yield significantly lower MAEs/MSEs of 0.55/0.20 and 0.51/0.23 kcal mol−1, respectively. [ABSTRACT FROM AUTHOR]

In the present work, we assess the effectiveness of singly differential cross sections (SDCS) due to electron-impact ionization by invoking the binary-encounter-Bethe (BEB) model on various atomic and molecular targets. The computed results were compared with the experimental and theoretical data. A good agreement was observed between the present and the available results. This agreement improves as the incident energy of the projectile increases. The model can be applied to compute the SDCS for the ions produced due to the electron-impact dissociative ionization process and the average energy due to the secondary electrons. Both these quantities are of interest in plasma processing and radiation physics. [ABSTRACT FROM AUTHOR]

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH2 group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH3 molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set. [ABSTRACT FROM AUTHOR]

The dihydroazulene/vinylheptafulvene (DHA/VHF) thermocouple is a promising candidate for thermal heat batteries that absorb and store solar energy as chemical energy without the need for insulation. However, in order to be viable the energy storage capacity and lifetime of the high energy form (i.e., the free energy barrier to the back reaction) of the canonical parent compound must be increased significantly to be of practical use. We use semiempirical quantum chemical methods, machine learning, and density functional theory to virtually screen over 230 billion substituted DHA molecules to identify promising candidates. We identify a molecule with a predicted energy density of 0.38 kJ/g, which is significantly larger than the 0.14 kJ/g computed for the parent compound. The free energy barrier to the back reaction is 11 kJ/mol higher than the parent compound, which should correspond to a half-life of about 10 days—4 months. This is considerably longer than the 3–39 h (depending on solvent) observed for the parent compound and sufficiently long for many practical applications. Our paper makes two main important contributions: (1) a novel and generally applicable methodological approach that makes screening of huge libraries for properties involving chemical reactivity with modest computational resources, and (2) a clear demonstration that the storage capacity of the DHA/VHF thermocouple cannot be increased to >0.5 kJ/g by combining simple substituents.

In the present work, we assess the effectiveness of singly differential cross sections (SDCS) due to electron-impact ionization by invoking the binary-encounter-Bethe (BEB) model on various atomic and molecular targets. The computed results were compared with the experimental and theoretical data. A good agreement was observed between the present and the available results. This agreement improves as the incident energy of the projectile increases. The model can be applied to compute the SDCS for the ions produced due to the electron-impact dissociative ionization process and the average energy due to the secondary electrons. Both these quantities are of interest in plasma processing and radiation physics.

The use of porous materials, aimed at increasing gas storage capacity at lower pressures, exploits physical adsorption and is an emerging strategy that is being widely investigated. In this scope, porous materials such as metal organic frameworks (MOFs) are a viable alternative, where structural modifications can enhance the properties of these materials and improve the degree of adsorption for a given gas. In this work, we evaluated the adsorption of methane, hydrogen, and hydrogen sulfide gases on pure isoreticular MOF (IRMOF)‐8 and aluminum‐doped IRMOF‐8 using density functional theory Perdew‐Burke‐Ernzerhof/DZVP and semiempirical AM1, PM3, PM6, PM6‐DH+, PM6‐DH2, PM6‐D3, and PM7 methods. Adsorption isotherms were calculated by means of Grand Canonical Monte Carlo simulations. It was found that doping did not provide a significant increase in the amount of adsorbed methane and hydrogen gases. Conversely, doping led to a considerable increase for hydrogen sulfide capture. [ABSTRACT FROM AUTHOR]

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH2 group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH3 molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set.

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Quantum mechanical (QM) methods have been gaining importance in structure‐based drug design where a reliable description of protein‐ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM‐based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM‐based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof‐of‐concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure‐based drug design. [ABSTRACT FROM AUTHOR]

Purification of the density matrix methods should be employed when dealing with complex chemical systems containing many atoms. The running times for these methods scale linearly with the number of atoms if we consider the sparsity from the density matrix. Since the efficiency expected from those methods is closely tied to the underlying parallel implementations of the linear algebra operations (e.g., P2 = P × P), we proposed a central processing unit (CPU) and graphics processing unit (GPU) parallel matrix-matrix multiplication in SVBR (symmetrical variable block row) format for energy calculations through the SP2 algorithm. This algorithm was inserted in MOPAC’s MOZYME method, using the original LMO Fock matrix assembly, and the atomic integral calculation implemented on it. Correctness and performance tests show that the implemented SP2 is accurate and fast, as the GPU is able to achieve speedups up to 40 times for a water cluster system with 42,312 orbitals running in one NVIDIA K40 GPU card compared to the single-threaded version. The GPU-accelerated SP2 algorithm using the MOZYME LMO framework enables the calculations of semiempirical wavefunction with stricter SCF criteria for localized charged molecular systems, as well as the single-point energies of molecules with more than 100.000 LMO orbitals in less than 1 h. [ABSTRACT FROM AUTHOR]

Obtaining reactivity information from the molecular electronic structure of a chemical system is a computationally intensive process. As a way of probing reactivity information around that, there exist electron density response variables, such as the Fukui functions (FFs), which are well‐established descriptors that summarize the local susceptibility to react. These properties only require few single‐point quantum chemical calculations, but even then, the intrinsic high cost and unfavorable computational complexity with respect to the number of atoms in the system makes this approach available only to small fragments and systems. In this study, we explore the computation of FFs, showing that semiempirical quantum chemical methods can be used to obtain the reactivity information equivalent to that of a Density Functional Theory (DFT) functional, for the eight entire polypeptide chains. The combination of semiempirical methods with the frozen orbital approximation allows for the obtention of these reactivity descriptors for biological systems with reasonable accuracy and speed, unlocking the utilization of these methods for such systems. These results for the frozen orbital approximation can be additionally improved when other molecular orbitals from the frontier band are employed in the computation. We also show the potential of this computational protocol in the ligand–protein complexes of HIV‐1 protease, predicting which of those ligands are active inhibitors. [ABSTRACT FROM AUTHOR]

Quantum mechanical (QM) semiempirical methods (SMs), combined with molecular mechanics (MM) force fields, are extensively used in theoretical studies of enzymatic reactions. Despite being several orders of magnitude faster than ab initio methods, their correctness is essential to be used in calculations requiring statistical simulations. Herein, a wide range of SMs are examined, from those based on s and p orbitals, sp-SMs (MNDO, AM1, PM3 and RM1), to those including d orbitals, spd-SMs, either based on approximations to the Hartree–Fock theory (MNDO/d, PM6 and AM1/d-PhoT) or derived from density functional theory (DFTB3). These QM Hamiltonians are used within a multiscale QM/MM additive scheme, to clarify their usefulness in mechanistic studies of phosphoryl-transfer reactions. The SN2-like reaction of the adenylyl group transfer catalysed by 4′-O-Nucleotidyltransferase (ANT4′) was selected as a benchmark. Geometrical characteristics of stationary structures, the shape of potential energy surfaces together with the barrier heights and kinetic isotope effects (KIEs), obtained with the different SMs/MM methods were compared with results obtained at higher M06-2X/MM level of theory. Critical limitations of the sp-SMs in the present mechanistic study were detected. The spd-SMs describe the reaction as a concerted process, same as the reference method M06-2X, but none of them is free of limitations. PM6 reproduces the biased trend of previous sp-SMs stabilizing structures of phosphorous atoms with certain pentavalent character, while AM1/d-PhoT and DFTB3 describe TSs more dissociative than M06-2X, which determines the lower quality of the computed primary and secondary 16O/18O KIEs. Efforts to improve the SMs can be guided by the exposure of their limitations, which were supported by the results of a second studied phosphoryl-transfer reactions; the hydrolysis of phosphodiester bond at the 3′-end of the viral DNA (vDNA). Thus, for instance, further increases in SMs accuracy can be achieved by improving the training and survey reference data sets, a more complete set of parameters for describing intermolecular interactions or further developments of spd-SMs. [ABSTRACT FROM AUTHOR]

The aim of this study was to analyze various theoretical models (clusters, systems with periodic boundary conditions) and methods, which could be applied to investigate the adsorption phenomena and for better interpretation of the experimental data. The density functional theory (DFT) and semiempirical (PM7) methods were used to model the adsorption phenomena at a surface of fumed nanooxides, silica gels, activated carbons, etc. The main idea is that appropriate theoretical analysis allows a deeper insight into interfacial phenomena related to the structure & properties of the adsorption layers vs. the textural and other characteristics of adsorbents. Comparison of the theoretically calculated characteristics with experimental ones can allow more accurate interpretation of the effects observed in various experiments on the adsorption phenomena. It was established that polarization of nonpolar and polar molecules adsorbed onto a polar surface and charge (& proton) transfer play an important role, as well as confined space effects. It enhances the interaction energy of adsorbed molecules bound to a solid surface and affects the surface orientation of adsorbed molecules, as well the behavior of the adsorption layer vs. temperature, pressure or concentration, as well other conditions. Surface hydrophobization reduces the interaction energy for both polar and nonpolar adsorbates. Adsorbates clusterization reduces the average energy of interaction of the adsorption layer with a surface per a molecule. The charge transfer is observed for both polar and nonpolar molecules interacting with polar surface functionalities. The mostly strong interfacial effects changing the behavior of the adsorption layer are observed upon proton transfer to the adsorbed molecules or vice versa. Variation in orientation of adsorbed molecules results in overestimation of the specific surface area estimated using a fixed value of surface area occupied by a probe molecule (e.g. 0.162 nm2 for N2). [ABSTRACT FROM AUTHOR]

This article analyzes the ability of semiempirical quantum‐mechanical methods (PM6 and PM7) and self‐consistent charge density‐functional tight‐binding (SCC‐DFTB) method DFTB3 to describe halogen bonds. Calculations of the electrostatic potential on the surface of molecules containing halogens show that the σ‐hole could be described well in modified neglect of diatomic overlap‐based methods. The situation is more complex in the case of DFTB3 where a simpler model is used for the electrostatics, but short‐ranged effects are covered in the Hamiltonian. All these methods can thus capture the effects that, for example, define the geometry of halogen bonds. The interaction energies are, however, affected by generally underestimated repulsion, which has been addressed earlier by standalone empirical corrections. Another approach to correcting this issue in DFTB3 is presented here—a modification of the energies of d‐orbitals on halogens yields better results than the empirical correction in DFTB3‐D3X, although it remains difficult to describe halogen and hydrogen bonds simultaneously. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract A chemical rationalization of the structural, thermodynamic, optical, fluorescence, and mechanical properties of concrete paving blocks was advanced. The results revealed that the values of Gibbs energy and enthalpy of the hydration reactions of the concretes prepared average −57.6 kJ mol−1 and -67.8 kJ mol−1, respectively. In addition, the results indicate that the processing of the concrete blocks with metakaolin as additive lead to hydrogen bond forming reactions. In this sense, both structural and thermodynamic properties of the hydrogen-bonded complexes showed that the presence of hydrogen bonding can be associated with the curing time of the concrete blocks. Further, by employing the fluorescence microscopy technique, the blue emission of the concrete materials was verified as a friendly strategy to evaluate their hydration reactions. In addition, optical microscopy experiments showed that all concrete paving blocks prepared are homogeneous. Furthermore, all concrete paving blocks with metakaolin as additive exhibit larger values of compressive strength (average 36.5 MPa) when compared to the corresponding blocks with absence of metakaolin (28.1 MPa). The addition of metakaolin also increased the cavity diameter of the concrete paving blocks in 10% when compared with the reference blocks. Finally, by considering structural, thermodynamic, optical and fluorescence properties, as well as, mechanical properties of compressive strength and abrasion resistance, the concrete paving block with the metakaolin addition of 10% present the largest potential to be applied to constructions. Graphical abstract Image 1 Highlights • A chemical rationalization of the processing of metakaolin concrete blocks was advanced. • The metakaolin concrete blocks are predicted to form hydrogen bonds with water molecules. • Fluorescence microscopy is a friendly strategy to evaluate concrete hydration reactions. • Optical microscopy revealed that all concrete blocks prepared are homogeneous. • The concrete with 10% of metakaolin presented the largest potential to be applied to constructions. [ABSTRACT FROM AUTHOR]

We present a computational characterisation of Aminotris(methylenephosphonic acid) (ATMP) and its potential use as an anionic partner for conductive ionic liquids (ILs). We argue that for an IL to be a good candidate for a conducting medium, two conditions must be fulfilled: (i) the charge must be transported by light carriers; and (ii) the system must maintain a high degree of ionisation. The result trends presented herein show that there are molecular ion combinations that do comply with these two criteria, regardless of the specific system used. ATMP is a symmetric molecule with a total of six protons. In the bulk phase, breaking the symmetry of the fully protonated state and creating singly and doubly charged anions induces proton transfer mechanisms. To demonstrate this, we used molecular dynamics (MD) simulations employing a variable topology approach based on the reasonably reliable semiempirical density functional tight binding (DFTB) evaluation of the atomic forces. We show that, by choosing common and economical starting compounds, we can devise a viable prototype for a highly conductive medium where charge transfer is achieved by proton motion.

Abstract A chemical rationalization of the loss of mass of concretes under rainy conditions, as well as the effects of the rain as water clusters on the structural and thermodynamic quantities of these materials are advanced. Results showed that the chemical equilibrium constants of the hydrations of calcium oxide and aluminum oxide are 1.00 × 1010 and 0.80, respectively. These values revealed that when the concretes were prepared, the hydration of calcium oxide (mainly due to the components of cement) was majority when compared with the hydration of aluminum oxide. Therefore, the unreacted materials were hydrated only when these concretes were under rainy conditions, which led to these materials to reduce mass. Further, structural and thermodynamic properties revealed that when the concretes are under rainy conditions, their main inorganic compounds are predicted to interact with water clusters via hydrogen bonding. From both structural and thermodynamic perspectives, the calcium hydroxide is predicted to form the most stable hydrogen-bonded complexes when the concretes are under rainy conditions. Finally, the ability of the main components of the concretes to form hydrogen bonding can be ordered as follows: Ca(OH) 2 » Al(OH) 3 ≈ SiO 2 » Fe 2 O 3. In this sense, the iron oxide can easily lose its hydrogen bonds with clusters of water, which tends to preserve the original properties of concrete when the rain is over. On the other hand, calcium hydroxide is predicted to form strong interactions with water clusters, that can be difficult to be broken when the rainy conditions are over, which can lead to pathological manifestations of the material. Graphical abstract Image 1 Highlights • A chemical rationalization of the loss of mass of the concretes under rainy conditions is advanced. • The effects of the rain on the structural and thermodynamic properties of concretes are evaluated. • The concretes under rainy conditions are predicted to interact with water clusters via hydrogen bonding. • Structural and thermodynamic properties revealed that Ca(OH) 2 is predicted to form stable hydrogen-bonded complexes. • The ability of the concrete components to form hydrogen bonds is ordered as follows: Ca(OH) 2 ≫ Al(OH) 3 ≈ SiO 2 ≫ Fe 2 O 3. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • This study is highly comprehensive: we have simulated almost 6000 trajectories of 1.6 ps length covering both N1H and N3H tautomers and both E and Z isomers of neutral UA. • We provide detailed insight into the excited-state lifetimes and into the photoisomerization and excited-state intramolecular proton-transfer (ESIPT) processes, which drive the radiationless deactivation of the electronically excited states of UA. • We find no evidence for an excitation-energy-dependent quantum yield for photoisomerization (EEDQY-PI) in isolated (E)-UA, as previously measured for (E)-UA in aqueous solutions, whereas we do find an EEDQY-PI for one tautomer of (Z)-UA. • For this tautomer of (Z)-UA, we also find an excitation-energy-dependent quantum yield for ESIPT (EEDQY-ESIPT), which is complementary to its EEDQY-PI. Abstract Urocanic acid (UA) is a UV filter found in human skin, which has been linked to photoimmunosuppression and the formation of skin cancer. Its UV-light-induced photoisomerization and radiationless deactivation mechanisms have been addressed previously by static calculations. In this paper, we present nonadiabatic trajectory-surface-hopping dynamics simulations of photoexcited UA using the semiempirical OM2/MRCI methodology and an adaptive-timestep algorithm. We have simulated almost 6000 trajectories, each for a simulation time of 1.6 ps, covering the entire conformational space of the E and Z isomers of both possible tautomers of the isolated neutral form of UA (overall 32 conformers). Initial conditions for the excited-state dynamics were obtained from 1 ns ground-state dynamics simulations. We find that UA has an ultrashort excited-state lifetime, which is due to ultrafast radiationless excited-state deactivation driven by E ↔ Z photoisomerization and excited-state intramolecular proton-transfer (ESIPT) processes. The computed S 1 excited-state lifetimes for the E and Z isomers of the N1H and N3H tautomers range from 271 to 506 fs. The photoisomerization quantum yield is calculated to be 43% (32%) for the combined E (Z) isomers of both tautomers. The shorter lifetime and the lower photoisomerization quantum yield of the Z isomers can be rationalized by the larger number of available excited-state deactivation processes: the Z isomers can undergo ESIPT and photoisomerization, whereas the E isomers can only deactivate via the latter process. The intramolecular hydrogen bond that is present in many Z conformers can prevent successful photoisomerization to an E isomer. We find no evidence for an excitation-energy-dependent quantum yield for photoisomerization (EEDQY-PI) in isolated (E)-UA, which has previously been detected spectroscopically in aqueous solution. However, we do find an EEDQY-PI as well as a complementary excitation-energy-dependent quantum yield for ESIPT (EEDQY-ESIPT) for the N1H- Z isomers, which demonstrates the competition of the photoisomerization and ESIPT processes. The present comprehensive study lays the groundwork for future photodynamics simulations of UA in the aqueous phase. [ABSTRACT FROM AUTHOR]

We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim benzoate groups, OAM and OAH, respectively). We employed free-energy perturbation (FEP) for relative binding energies at the molecular mechanics (MM) and the combined quantum mechanical (QM) and MM (QM/MM) levels, the latter obtained with the reference-potential approach with QM/MM sampling for the MM → QM/MM FEP. The semiempirical QM method PM6-DH+ was employed for the ligand in the latter calculations. Moreover, binding free energies were also estimated from QM/MM optimised structures, combined with COSMO-RS estimates of the solvation energy and thermostatistical corrections from MM frequencies. They were performed at the PM6-DH+ level of theory with the full host and guest molecule in the QM system (and also four water molecules in the geometry optimisations) for 10-20 snapshots from molecular dynamics simulations of the complex. Finally, the structure with the lowest free energy was recalculated using the dispersion-corrected density-functional theory method TPSS-D3, for both the structure and the energy. The two FEP approaches gave similar results (PM6-DH+/MM slightly better for OAM), which were among the five submissions with the best performance in the challenge and gave the best results without any fit to data from the SAMPL5 challenge, with mean absolute deviations (MAD) of 2.4-5.2 kJ/mol and a correlation coefficient (R2) of 0.77-0.93. This is the first time QM/MM approaches give binding free energies that are competitive to those obtained with MM for the octa-acid host. The QM/MM-optimised structures gave somewhat worse performance (MAD = 3-8 kJ/mol and R2 = 0.1-0.9), but the results were improved compared to previous studies of this system with similar methods. [ABSTRACT FROM AUTHOR]

A chemical rationalization of the processing and application of the roughcast and plaster mortar coatings was advanced. The results revealed that the structural and thermodynamic nature of the hydrogen-bonded complexes between the inorganic precursors and water molecules are associated with the physical properties of both coatings. In this sense, the workability and curing time of the roughcast and the plaster mortars studied, seemingly, are related to the nature of the water solvation in the main components of these materials: calcium hydroxide and silicon dioxide. In addition, PM7 and PM7/COSMO results indicate that the enthalpy of solvation of water by hydrogen bonds in calcium hydroxide is stronger when compared with silicon dioxide systems. Therefore, the presence of free hydrated lime (calcium hydroxide) in the precursor mixture of plaster mortar leads to the large workability and elapsed curing time of this material. On the other hand, the absence of free hydrated lime in the precursor mixture of the roughcast mortar leads to its poor workability and faster elapsed curing time. Further, fluorescence microscopy experiments revealed that the inorganic compounds present in the cement precursor were transformed into different materials, that exhibit red and blue fluorescence. Finally, mechanical tests showed a tensile strength average 0.67 MPa for the plaster mortar material, whereas for the roughcast material is 0.53 MPa. [ABSTRACT FROM AUTHOR]

Computational investigation of the photochemical properties of transition‐metal‐centered dyes typically involves optimization of the molecular structure followed by calculation of the UV/visible spectrum. At present, these steps are usually carried out using density functional theory (DFT) and time‐dependent DFT calculations. Recently, we demonstrated that semiempirical methods with appropriate parameterization could yield geometries that were in very good agreement with DFT calculations, allowing large sets of molecules to be screened quickly and efficiently. In this article, we modify a configuration interaction (CI) method based on a semiempirical PM6 Hamiltonian to determine the UV/visible absorption spectra of Ru‐centered complexes. Our modification to the CI method is based on a scaling of the two‐center, two‐electron Coulomb integrals. This modified, PM6‐based method shows a significantly better match to the experimental absorption spectra versus the default configuration interaction method (in MOPAC) on a training set of 13 molecules. In particular, the modified PM6 method blue‐shifts the location of the metal‐to‐ligand charge‐transfer (MLCT) peaks, in better agreement with experimental and DFT‐based computational results, correcting a significant deficiency of the unmodified method. Published 2018. This article is a U.S. Government work and is in the public domain in the USA [ABSTRACT FROM AUTHOR]

Semiempirical quantum chemistry methods offer a very interesting compromise between accuracy and computational complexity. The low-frequency vibration modes of three crystalline materials, namely, polyethylene, poly(vinylidene fluoride) form II, and α-D-glucose, have been studied using the PM6 and PM7 Hamiltonians in order to assess the performance of NDDO methods in the interpretation of terahertz spectra. The results have been compared with the available experimental data and former calculations performed using alternative methods. NDDO calculations are in good qualitative or semiquantitative agreement with the experimentally observed terahertz spectra. [ABSTRACT FROM AUTHOR]

Various quantum chemical approaches including ab initio, density functional theory (B3LYP, CAM-B3LYP, mB97X-D, M06HF) and semiempirical (PM7) methods with different basis sets and various solvation models (SMD, IEFPCM, COSMO), as well as a supermolecular approach, and the basis set superposition error (BSSE) corrections, used to analyze the solvation effects are compared for polar (water, ethanol, dimethylsulfoxide, acetonitrile, acetone), weakly polar (chloroform) and nonpolar (benzene, n-hexane, carbon tetrachloride) solvents per se and interacting with unmodified and modified silicas. The DFT methods give smaller errors in the AGs values than the PM7 method with various solvation models. For the molecular clusters with water alone or water with organics, the interaction energy decreases with enhanced amorphism of the systems. The supermolecular approach with PM7 gives worse results (in comparison to the experimental data) than those of SMD/PM7 or COSMO/PM7. An increase in the basis sets can give worse results than that at smaller ones because the parameters in the SMD model were calibrated using the experimental data and ab initio or DFT calculations of the same systems with relatively small basis sets. [ABSTRACT FROM AUTHOR]

Host–guest interactions of tyrosine with β-cyclodextrin have been investigated by the semiempirical methods PM7, PM6 and its modern variants, PM6-DH2, PM6-D3H4, and the ONIOM2 hybrid approach and density functional theory with the B3LYP functional. Two models were assessed for the encapsulation of tyrosine in the cavity of β-cyclodextrin. The results obtained with semiempirical models clearly indicate that the complexation process with the A model (Tyrosine enters into the cavity of β-CD from its wide side by hydroxyl phenolic group) is energetically favored than that of the B model (Tyrosine penetrates the β-CD cavity from its wide side by carboxylic group), the preference is greater in the case of ONIOM2 calculations. In addition, NBO analysis reveals that mutual interactions between donor and acceptor orbital of tyrosine and β-CD play an important role to the stabilization of such complex. Finally, 1 H Nuclear Magnetic Resonance (NMR) chemical shifts of free and complexed tyrosine were calculated by the gauge-including atomic orbital (GIAO) method and compared with available experimental data. [ABSTRACT FROM AUTHOR]

The excited states of perylene-based dye aggregates were investigated with emphasis on the description of the potential energy surfaces for the intermolecular motion in a dimer, which are of importance for exciton trapping. The aim is to investigate the applicability of TDDFT and semiempirical methods. The longitudinal displacement of two π-stacked molecules against each other is used as model and the methods are benchmarked against SCS-CC2 and SCS-ADC(2). Furthermore a simple character analysis is applied. In the case of the perylene dimer, CAM-B3LYP and ωB97XD provide accurate results. However, while CAM-B3LYP fails for the PBI (perylene bisimide) dimer the performance of ωB97XD is highly dependent on the used monomer geometry due to close-lying diabatic states. A change in geometry changes the character of the excited states even qualitatively. The accuracy of several other long-range corrected functionals (LC-BLYP, LC- ωPBE, ωB97X) and the effect of empirically tuning the range-separation parameter of ωB97XD are also presented for this interesting case. Furthermore, it is shown that the semiempirical method OM2 fails to provide a correct description of the excited states when the orbital overlap plays a significant role. This is attributed to the too contracted basis set. [ABSTRACT FROM AUTHOR]

The thermal expansion coefficient (α exp. ), the molecular volume (V m ), the entropy of surface formation (S a ), and the Gibbs energy of surface formation (E a ) of four pentaalkylguanidinium-based MILs [C n TMG][FeCl 3 Br] (n=2, 4, 6, 8) were calculated based on the density and surface tension data determined from 278.15 to 323.15 K. In terms of classical semiempirical methods, the standard molar entropy (S 0 ), the lattice energy (U POT ), the molar enthalpy of evaporation (Δg lH0 m(T b ), Δg lH0 m(298 K)), and the thermal expansion coefficient (α est. ) of the MILs were further estimated. The estimation results indicate that the classical semiempirical methods are suitable for estimating the thermophysical properties of the MILs, except the unusual α exp. , which were extremely larger than those of representative non-magnetic ionic liquids (ILs). We further optimized the estimation methods and discussed the potential reasons for the unusual thermal expansion coefficient of the MILs., (© 2023 Wiley-VCH GmbH.)

The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6–0.7 pH units. For carboxylic acids, the accuracy (0.7–1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5–0.6), slightly worse (0.5–1.0), and worse (1.0–2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2–5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10–15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4–5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process.

Theoretical analysis of formation energy and geometry was done to compare the relative stabilities of modified carbon nanostructures representative fragments. Structure and energies of formation were calculated at semiempirical level of theory. Depending of B-N pair localization on the molecular structures the formation enthalpy decreases. B-N substitution in tubular structures at low concentration decreases the energy when the tubes have small diameters. Our results are in according to experimental works which have shown that boron and nitrogen are met at region of defects in B X C Y N Z nanostructures.

Semiempirical AM1 and INDO/CIS methods were used to study the structures and spectroscopy of hydrogen bonded complexes formed by the oligophenyleneethynylene (monomer A) with isophthalic acid (monomer B). The binding energies of the complexes are lowered by increasing electron-donating abilities of the substituents near the hydrogen bonds on monomer A. The first absorptions in the electronic spectra and the vibration frequencies of the N-H bonds in the IR spectra for the complexes are both red-shifted compared with those of the monomers. The presence of dimethylsulfoxide (DMSO) can reduce the binding energy of the complex through hydrogen bonding. This results in a blue-shift for the first absorption in the electronic spectrum and red-shift for the vibration frequencies of the N-H bonds in the IR spectrum of the complex.

In this work, we tested the PM6, PM6-DH+, PM6-D3, and PM7 enthalpies of formation in aqueous solution as scoring functions across 33 decoy sets to discriminate native structures or good models in a decoy set. In each set these semiempirical quantum chemistry methods were compared according to enthalpic and geometric criteria. Enthalpically, we compared the methods according to how much lower was the enthalpy of each native, when compared with the mean enthalpy of its set. Geometrically, we compared the methods according to the fraction of native contacts ( Q), which is a measure of geometric closeness between an arbitrary structure and the native. For each set and method, the Q of the best decoy was compared with the Q0, which is the Q of the decoy closest to the native in the set. It was shown that the PM7 method is able to assign larger energy differences between the native structure and the decoys in a set, arguably because of a better description of dispersion interactions, however PM6-DH+ was slightly better than the rest at selecting geometrically good models in the absence of a native structure in the set. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Lignosulphonates (LS), also known as lignin sulfonates or sulfite lignin, are lignins in sulfonated forms, obtained from the 'sulfite liquors,' a residue of the wood pulp extraction process. Their main utility lies in its wide range of properties, they can be used as additives, dispersants, binders, fluxing, binder agents, etc. in fields ranging from food to fertilizer manufacture and even as agents in the preparation of ion exchange membranes. Since they can be manufactured relatively easy and quickly, and that its molecular size can be manipulated to obtain fragments of very low molecular weight, they are used as transport agents in the food industry, cosmetics, pharmaceutical and drug development, and as molecular elements for the treatment of health problems. In this paper, we study the electronic structural and optical characteristics of LS incorporating ammonium, sulfur, calcium, and sodium ions in acidic and basic aqueous media in order to gain a better understanding of their behavior and the very interesting properties exhibit. The studies were performed using the molecular modeling program HyperChem 5 using the semiempirical method PM3 of the NDO Family (neglect of differential overlap), to calculate the structural properties. We calculated the electronic and optical properties using the semiempirical method ZINDO / CI. [ABSTRACT FROM AUTHOR]

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling 'modified divide-and-conquer' model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

An accurate model of three-dimensional protein structure is important in a variety of fields such as structure-based drug design and mechanistic studies of enzymatic reactions. While the entries in the Protein Data Bank () provide valuable information about protein structures, a small fraction of the PDB structures were found to contain anomalies not reported in the PDB file. The semiempirical PM7 method in MOPAC2012 was used for identifying anomalously short hydrogen bonds, C-H⋯O/C-H⋯N interactions, non-bonding close contacts, and unrealistic covalent bond lengths in recently published Protein Data Bank files. It was also used to generate new structures with these faults removed. When the semiempirical models were compared to those of PDB_REDO (), the clashscores, as defined by MolProbity (), were better in about 50 % of the structures. The semiempirical models also had a lower root-mean-square-deviation value in nearly all cases than those from PDB_REDO, indicative of a better conservation of the tertiary structure. Finally, the semiempirical models were found to have lower clashscores than the initial PDB file in all but one case. Because this approach maintains as much of the original tertiary structure as possible while improving anomalous interactions, it should be useful to theoreticians, experimentalists, and crystallographers investigating the structure and function of proteins. [ABSTRACT FROM AUTHOR]

The aim of this work was to study the interaction between the local anesthetic benzocaine and p-sulfonic acid calix[ n]arenes using NMR and theoretical calculations and to assess the effects of complexation on cytotoxicity of benzocaine. The architectures of the complexes were proposed according to 1H NMR data (Job plot, binding constants, and ROESY) indicating details on the insertion of benzocaine in the cavity of the calix[ n]arenes. The proposed inclusion compounds were optimized using the PM3 semiempirical method, and the electronic plus nuclear repulsion energy contributions were performed at the DFT level using the PBE exchange/correlation functional and the 6-311G(d) basis set. The remarkable agreement between experimental and theoretical approaches adds support to their use in the structural characterization of the inclusion complexes. In vitro cytotoxic tests showed that complexation intensifies the intrinsic toxicity of benzocaine, possibly by increasing the water solubility of the anesthetic and favoring its partitioning inside of biomembranes. [ABSTRACT FROM AUTHOR]

Two approaches to treat solvent polarization and reorientation effects for excited states of molecules and surfaces have been implemented in the recently developed MSINDO-sCIS method (Gadaczek, Krause, Hintze, Bredow, J. Chem. Theory Comput. 2011, 7, 3675). They allow for an efficient calculation of analytical energy gradients and hence open the opportunity to investigate fluorescence effects or photochemical reactions in solution for large molecules that are difficult to treat with high-level methods. Both approaches are based on the conductor-like screening model (COSMO) (Klamt and Schüürmann, J. Chem. Soc., Perkin Trans. 1993, 2, 799) in combination with the configuration interaction singles (CIS) method (Foresman, Head-Gordon, Pople, and Frisch, J. Phys. Chem. 1992, 96, 135). The paper gives a brief outline of the theoretical background. As a first application, solvent shifts of three well-studied, environment-sensitive fluorescent dyes (Kucherak, Didier, Mély, and Klymchenko, J. Phys. Chem. Lett. 2010, 1, 616) have been calculated and compared with experimental results and standard time-dependent density functional theory. A statistical evaluation of MSINDO-COSMO-sCIS is provided for a set of 39 molecules suggested recently by Jacquemin et al. (Jacquemin, Planchat, Adamo, and Mennucci, J. Chem. Theory Comput. 2012, 8, 2359). Calculated vertical and adiabatic excitation energies and fluorescence energies are compared to experimental data. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]