Semiempirical Computational Methods Research Articles

SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes

Accurate estimation of protein–ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms. To validate it rigorously, we have compiled and made available the PL-REX benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets. Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more expensive DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R2 = 0.69) and exhibits consistent performance across all targets. In contrast to DFT, SQM2.20 provides affinity predictions in minutes, making it suitable for practical applications in hit identification or lead optimization.

Theoretical study to determine the band gap of the bis(benzoylacetone)zirconium complex compound using the PM3 semi-empirical computational method

Theoretical study to determine the band gap of the bis(benzoylacetone)zirconium complex compound using the PM3 semi-empirical computational method

Computational strategies to model the interaction and the reactivity of biologically-relevant transition metal complexes

Transition metal atoms possess the unique capacity to induce significant changes in the electronic structure of their ligands, often culminating in substantial modification of their chemical behavior, and this ability explains well their evolutionary incorporation into the living matter. Exactly this complexity of metal atom behaviours on the electronic level is the reason of various quantum chemistry strategies developed for their description. On the other hand, the application of quantum chemistry methodologies for gaining a comprehensive understanding of the interaction between metal and biological matter can only be approached through adequate modelling of the chemical phenomena in object, sometimes also requiring the support of classical or semiempirical computational methods. This minireview features the tactics developed in our group for analyzing the modus operandi of “transition metals in biology” in various settings: in the active sites of proteins, in the physiological solutions, and incorporated in metallodrug scaffolds.

π-Electron delocalization and electronic transitions in oligomeric and polymeric phthalocyanine zinc(II) complexes. Part 1: Linear oligo- and one-dimensional polyphthalocyanines

In this Part 1 of our two part study, 1D-linear oligomeric phthalocyanine zinc(II) with fully annulated (fused) phthalocyanine macrocycles are described. By semi-empirical and DFT computational methods the UV-vis and near infrared spectra, including energy gaps, are thoroughly evaluated. The long-wavelength Q band of the oligophthalocyanines is compared with the long wavelength absorption band of analogous oligoacenes consisting of annulated benzene rings. In addition, graphene nanoribbons are considered. The aromaticity is especially interesting when considering Clar’s rule. Therefore it is the aim to get information about the extent of [Formula: see text]-electron delocalization in linear or semi-linear systems. Finally, the results of linear oligophthalocyanines are extrapolated to estimate the energy gap of 1D linear polyphthalocyanine by DFT, and the result is compared to the DFT calculation of the periodic structure with a plane-wave basis set. Part 2 will describe non-linear oligo- and two-dimensional polyphthalocyanines.

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD.

2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an in situ structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semiempirical computational methods, demonstrating that the Fe(III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and +171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox-difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

Dynamic equilibrium evaluation for planing hulls with arbitrary geometry and variable deadrise angles – The Virtual Prismatic Hulls Method

This paper describes the development of a semi-empirical computational method to solve the dynamic equilibrium problem for planing hulls with arbitrary geometry, including variable deadrise angles along the length. The method is based on Savitsky׳s method (1964) and it is named ‘Virtual Prismatic Hulls Method’, allowing for the determination of the intensity of the lift force and the resulting center of pressure, in order to determine the dynamic equilibrium position and the drag force, at the fully developed planing regime, for any arbitrary, non-prismatic hard chine hull form. Results produced by the method are presented and investigated and their applicability is established and compared with experimental results of well-known systematic series of planing boats.

Kumada cross coupling reaction based synthesis, antimicrobial and computational studies of 6-aryl-2-phenyl-3-methylquinazolin-4(3H)-ones

Nickel catalyzed Kumada cross coupling reaction, a novel synthetic method for the synthesis of 6-aryl-2-phenyl-3-methylquinazolin-4(3H)-ones (6a–6i), was carried out by condensing 6-iodo-2-phenyl-3-methyl-quinazolin-4(3H)-one (4) with various 6-aryl/heteroaryl Grignard reagents. Molecular properties of compounds 4 and 6a–6i were studied using semiempirical PM3 computational method. The optimized geometry of the product 6 indicated that the aryl group at the position 6 was not coplanar with respect to either quinazolinone ring or phenyl group at 2 position. Compounds 6a–6i were screened for their activity against bacteria and fungi.

Thermodynamic analysis of fuels in gas phase: ethanol, gasoline and ethanol - gasoline predicted by DFT method.

This paper presents a theoretical study using density functional theory to calculate thermodynamics properties of major molecules compounds at gas phase of fuels like gasoline, ethanol, and gasoline-ethanol mixture in thermal equilibrium on temperature range up to 1500K. We simulated a composition of gasoline mixture with ethanol for a thorough study of thermal energy, enthalpy, Gibbs free energy, entropy, heat capacity at constant pressure with respect to temperature in order to study the influence caused by ethanol as an additive to gasoline. We used semi-empirical computational methods as well in order to know the efficiency of other methods to simulate fuels through this methodology. In addition, the ethanol influence through the changes in percentage fractions of chemical energy released in combustion reaction and the variations on thermal properties for autoignition temperatures of fuels was analyzed. We verified how ethanol reduces the chemical energy released by gasoline combustion and how at low temperatures the gas phase fuels in thermal equilibrium have similar thermodynamic behavior. Theoretical results were compared with experimental data, when available, and showed agreement. Graphical Abstract Thermodynamic analysis of fuels in gas phase.

A computational method for the systematic screening of reaction barriers in enzymes: searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate.

We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on the barrier height of an enzymatic reaction. The intent of this method is not a quantitative prediction of the barrier heights, but rather to identify promising mutants for further computational or experimental study. The method is applied to identify promising single and double mutants of Bacillus circulans xylanase (BCX) with increased hydrolytic activity for the artificial substrate ortho-nitrophenyl β-xylobioside (ONPX2). The estimated reaction barrier for wild-type (WT) BCX is 18.5 kcal/mol, which is in good agreement with the experimental activation free energy value of 17.0 kcal/mol extracted from the observed kcat using transition state theory (Joshi et al., 2001). The PM6 reaction profiles for eight single point mutations are recomputed using FMO-MP2/PCM/6-31G(d) single points. PM6 predicts an increase in barrier height for all eight mutants while FMO predicts an increase for six of the eight mutants. Both methods predict that the largest change in barrier occurs for N35F, where PM6 and FMO predict a 9.0 and 15.8 kcal/mol increase, respectively. We thus conclude that PM6 is sufficiently accurate to identify promising mutants for further study. We prepared a set of all theoretically possible (342) single mutants in which every amino acid of the active site (except for the catalytically active residues E78 and E172) was mutated to every other amino acid. Based on results from the single mutants we construct a set of 111 double mutants consisting of all possible pairs of single mutants with the lowest barrier for a particular position and compute their reaction profile. None of the mutants have, to our knowledge, been prepared experimentally and therefore present experimentally testable predictions.

Computational study on the structure and properties of ternary complexes of Ln3+ (Ln = La, Ce, Nd AND Sm) with 5,7-dichloroquinoline-8-ol and 4-vinyl pyridine

In the present research, we have mainly concentrated on the survey of interactions in Ln3+ (Ln = La, Ce, Nd, and Sm) ternary complexes of 5,7-dichloroquinoline-8-ol (DCQ) and 4-vinyl pyridine (VP), [Ln(VP)2(DCQ)3]3+ by means of density functional theory, Hartree-Fock and Sparkle/PM3 semi-empirical computational methods. For VP and DCQ ligands, the cation binding energy sequence follows the order La3+ > Ce3+ > Nd3+ > Sm3+ as expected based on increasing in the hardness and decreasing in the ionic radius of this lanthanide cation series. A similar trend was observed in the calculated binding energy of the aforesaid ligands with the hydrated lanthanide cation series [Ln(H2O)9]3+, while the computed values of deformation energy of ligands upon complexation demonstrated an opposite order in the lanthanide cation series. Moreover, the solvent effects are considered via a polarized continuum model and provided a significant increase in the binding strength while the relative magnitude of binding energies is the same as that in the gas phase. Combining quantum and statistical mechanical calculations, we have also determined quantitatively a reliable estimate of the conformational distribution of the [Sm(VP)2(DCQ)3]3+ complex at various temperatures in the gas phase by computing the molecular partition functions and consequently the analysis of the conformational equilibrium constants.

Noninnocence in Metal Complexes: A Dithiolene Dawn

Noninnocence in inorganic chemistry traces its roots back half a century to work that was done on metal complexes containing unsaturated dithiolate ligands. In a flurry of activity in the early 1960s by three different research groups, homoleptic bis and tris complexes of these ligands, which came to be known as dithiolenes, were synthesized, and their structural, electrochemical, spectroscopic, and magnetic properties were investigated. The complexes were notable for facile one-electron transfers and intense colors in solution, and conventional oxidation-state descriptions could not account for their electronic structures. The bis complexes were, in general, found to be square-planar, including the first examples of this geometry for paramagnetic complexes and different formal d(n) configurations. Several of the neutral and monoanionic tris complexes were found to have trigonal-prismatic coordination, the first time that this geometry had been observed in molecular metal complexes. Electronic structural calculations employing extended Hückel and other semiempirical computational methods revealed extensive ligand-metal mixing in the frontier orbitals of these systems, including the observation of structures in which filled metal-based orbitals were more stable than ligand-based orbitals of the same type, suggesting that the one-electron changes upon oxidation or reduction were occurring on the ligand rather than on the metal center. A summary of this early work is followed with a brief section on the current interpretations of these systems based on more advanced spectroscopic and computational methods. The take home message is that the early work did indeed provide a solid foundation for what was to follow in investigations of metal complexes containing redox-active ligands.

Stabilization of a Protein Nanocage through the Plugging of a Protein–Protein Interfacial Water Pocket

The unique structural properties of the ferritin protein cages have provided impetus to focus on the methodical study of these self-assembling nanosystems. Among these proteins, Escherichia coli bacterioferritin (EcBfr), although architecturally very similar to other members of the family, shows structural instability and an incomplete self-assembly behavior by populating two oligomerization states. Through computational analysis and comparison to its homologues, we have found that this protein has a smaller than average dimeric interface on its 2-fold symmetry axis mainly because of the existence of an interfacial water pocket centered around two water-bridged asparagine residues. To investigate the possibility of engineering EcBfr for modified structural stability, we have used a semiempirical computational method to virtually explore the energy differences of the 480 possible mutants at the dimeric interface relative to that of wild-type EcBfr. This computational study also converged on the water-bridged asparagines. Replacing these two asparagines with hydrophobic amino acids resulted in proteins that folded into α-helical monomers and assembled into cages as evidenced by circular dichroism and transmission electron microscopy. Both thermal and chemical denaturation confirmed that, in all cases, these proteins, in agreement with the calculations, possessed increased stability. One of the three mutations shifts the population in favor of the higher-order oligomerization state in solution as evidenced by both size exclusion chromatography and native gel electrophoresis. These results taken together suggest that our low-level design was successful and that it may be possible to apply the strategy of targeting water pockets at protein--protein interfaces to other protein cage and self-assembling systems. More generally, this study further demonstrates the power of jointly employing in silico and in vitro techniques to understand and enhance biostructural energetics.

Demonstration and interpretation of significant asymmetry in the low-resolution and high-resolution Q y fluorescence and absorption spectra of bacteriochlorophyll a

Low- and high-resolution absorption and fluorescence emission Q(y) spectra of bacteriochlorophyll a (BChl a) were recorded, along with homogeneous band line shapes, revealing significant asymmetry between the absorption and emission profiles that are interpreted using a priori spectral calculations. The spectra were recorded in a range of organic solvents facilitating both penta- and hexa-coordination of Mg at ambient and cryogenic temperatures. Detailed vibrational structure in the ground electronic state, virtually independent of Mg coordination, was revealed at 4.5 K by a hole-burning fluorescence line-narrowing technique, complementing the high-resolution spectrum of the excited state measured previously by hole burning to provide the first complete description of the Q(y) absorption and fluorescence spectra of BChl a. Spectral asymmetry persists from 4.5 to 298 K. Time-dependent density-functional theory calculations of the gas-phase absorption and emission spectra obtained using the CAM-B3LYP density functional, curvilinear coordinates, and stretch-bend-torsion scaling factors fitted to data for free-base porphyrin quantitatively predict the observed frequencies of the most-significant vibrational modes as well as the observed absorption∕emission asymmetry. Most other semi-empirical, density-functional, and ab initio computational methods severely overestimate the electron-vibrational coupling and its asymmetry. It is shown that the asymmetry arises primarily through Duschinsky rotation.

Theoretical studies of 2-nitrobenzaldehyde and furan-2-carbaldehyde Schiff base of 2-amino pyridine

The vibration modes of the title compounds are examined by experimentally and theoretically using the semi-empirical AM1 and PM3 computational methods. Vibration modes for 2N-(2-nitro benzalidine) amino pyridine (2-NBAPy), the correlation coefficients obtained for AM1 and PM3 methods are 0.996483 and 0.992236, respectively. However, vibration modes for 2N-(Furfural) amino pyridine (FAPy), the correlation coefficients for AM1 and PM3 methods are 0.993238 and 0.990477, respectively. AM1 method provides most satisfactory correlations between experimental and calculated fundamental vibration modes of title compounds (CC=0.996483 and 0.993238, respectively).

Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants Using Semi-Empirical Computational Methods

AbstractPerfluorinated acids (PFAs) are contaminants detected worldwide in a range of abiotic and biotic environmental matrices. The two major classes of PFAs include the perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), both of which are considered persistent and potentially bioaccumulative. Current research and regulatory efforts are focussed on the straight-chain members of each PFA class and homologue group, primarily because these congeners are the major components of technical mixtures and are also available as pure standards. However, the numerous potential branched congeners in each PFA class represent a poorly understood family of environmental contaminants whose environmental and toxicological properties may be more important than the more prevalent straight-chain members. To help broaden the current understanding of PFA environmental fate and toxicology, semi-empirical computational methods were used predict fundamental physico-chemical properties of all potential C4 to C8 PCFA and PFSA congeners. Established quantitative structure-activity models for other multi-class emerging and legacy contaminants were applied to estimate key parameters related to the toxicology, environmental partitioning, and abiotic and biotic degradation mechanisms for each PFA class. The findings provide guidance for developing new analytical methods for separating and identifying PFAs in environmental and technical mixtures, prioritizing efforts on synthesizing authentic standards, and focussing toxicological studies on the congeners most likely to be of concern.

Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants Using Semi-Empirical Computational Methods

Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants Using Semi-Empirical Computational Methods

Intermolecular resonant energy transfer of oligo( p-phenylenevinylene)–fullerene dyads: A theoretical study

Intermolecular resonant energy transfer (RET) of three different oligo( p-phenylenevinylene)–fullerene dyads (OPV n –MPC 60; n = 2–4) has been studied by using semiempirical computational methods. Sub-picosecond intermolecular energy transfer comparable to intramolecular energy transfer has been found to take place in horizontal and vertical directions between adjacent dyads. The results do not rule out the possibility that energy transfer could precede charge separation in thin films made of OPV n –MPC 60.

New Ruthenium Complexes Containing Oligoalkylthiophene‐Substituted 1,10‐Phenanthroline for Nanocrystalline Dye‐Sensitized Solar Cells

AbstractTwo new ruthenium complexes [Ru(dcbpy)(L)(NCS)2], where dcbpy is 4,4′‐dicarboxylic acid‐2,2′‐bipyridine and L is 3,8‐bis(4‐octylthiophen‐2‐yl)‐1,10‐phenanthroline (CYC‐P1) or 3,8‐bis(4‐octyl‐5‐(4‐octylthiophen‐2‐yl)thiophen‐2‐yl)‐1,10‐phenanthroline (CYC‐P2), are synthesized, characterized by physicochemical and semiempirical computational methods, and used as photosensitizers in nanocrystalline dye‐sensitized solar cells. It was found that the difference in light‐harvesting ability between CYC‐P1 and CYC‐P2 is associated mainly with the location of the frontier orbitals, in particular the highest occupied molecular orbital (HOMO). Increasing the conjugation length of the ancillary ligand decreases the energy of the metal‐to‐ligand charge transfer (MLCT) transition, but at the same time reduces the molar absorption coefficient, owing to the HOMO located partially on the ancillary ligand of the ruthenium complex. The incident photon‐to‐current conversion efficiency curves of the devices are consistent with the MLCT band of the complexes. Therefore, the overall efficiencies of CYC‐P1 and CYC‐P2 sensitized cells are 6.01 and 3.42 %, respectively, compared to a cis‐di(thiocyanato)‐bis(2,2′‐bipyridyl)‐4,4′‐dicarboxylate ruthenium(II)‐sensitized device, which is 7.70 % using the same device‐fabrication process and measuring parameters.

Improved Prediction of Heats of Formation of Energetic Materials Using Quantum Mechanical Calculations

We present simple atom and group-equivalent methods that will convert quantum mechanical energies of molecules to gas phase heats of formation of CHNO systems. In addition, we predict heats of sublimation and vaporization derived from information obtained from the quantum-mechanically calculated electrostatic potential of each isolated molecule. The heats of sublimation and vaporization are combined with the aforementioned gas phase heats of formation to produce completely predicted condensed phase heats of formation. These semiempirical computational methods, calibrated using experimental information, were applied to a series of CHNO molecules for which no experimental information was used in the development of the methods. These methods improve upon an earlier effort of Rice et al. [Rice, B. M.; Pai, S. V.; Hare, J. Combust. Flame 1999, 118, 445] through the use of a larger basis set and the application of group equivalents. The root-mean-square deviation (rms) from experiment for the predicted group-equivalent gas phase heats of formation is 3.2 kcal/mol with a maximum deviation of 6.5 kcal/mol. The rms and maximum deviation of the predicted liquid heats of formation are 3.2 and 7.4 kcal/mol, respectively. Finally, the rms and maximum deviation of predicted solid heats of formation are 5.6 and 12.2 kcal/mol, respectively, an improvement in the rms of approximately 40% compared to the earlier Rice et al. predictions using atom equivalents and a smaller basis set (B3LYP/6-31G*).

New mean-energy formulae for free energy differences

We report a number of new exact expressions, within the realm of classical statistical mechanics, for the solvation contribution ΔA to the free energy change of a solute that undergoes a transformation between two states that differ in the way they interact with the solvent. Our basic result is a coupling-parameter expression that is equivalent to the usual cumulant expansion of ΔA. In our formula, which is derived from a linear coupling-parameter scheme, all the cumulant terms beyond the first one are collected into an integral over the coupling parameter. From this formula, with the help of the mean-value theorems of calculus, we derive exact one- and two-reference-point mean-energy expressions for the solvation free energy change, neither of which is limited to the linear response regime. Both the one- and the two-reference point formulae are given in terms of one distinguished value of the coupling parameter ( and ξ*, respectively) that is not known a priori (except in the linear response regime where we find it exactly). In the case of the two-reference-point formula, we relate ξ* with the cumulative changes of the solvation structure along the intermediate states sampled in the (ξ = 0) → (ξ = 1) transformation of the solute. Finally, and based on these developments, we present an analysis of the Linear Interaction Energy and of the Extended Linear Response semi-empirical computational methods (widely used for the determination of binding constants of ligand/receptor biological systems) in an effort to understand their statistical mechanical foundations as well as their domain of applicability.