Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field (SCF) Implementation

On the Topological Phase around Conical Intersections with Tamm-Dancoff Linear-Response Time-Dependent Density Functional Theory

Regions of nuclear-configuration space away from the Franck-Condon geometry can prove problematic for some electronic structure methods, given the propensity of such regions to possess conical intersections, i.e., (highly connected) points of degeneracy between potential energy surfaces. With the likelihood (perhaps even inevitability) for nonadiabatic dynamics simulations to explore molecular geometries in close proximity to conical intersections, it is vital that the performance of electronic structure methods is routinely examined in this context. In a recent paper [Taylor, J. T. J. Chem. Phys. 2023, 159, 214115.], the ability of linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) to provide a proper description of conical intersections, in terms of their topology and topography, was investigated, with particular attention paid to conical intersections between two excited electronic states. For the same prototypical molecules, protonated formaldimine and pyrazine, we herein consider whether AA LR-TDDFT can correctly reproduce the topological phase accumulated by the adiabatic electronic wave function upon traversing a closed path around an excited-to-excited state conical intersection despite not using the appropriate quadratic-response nonadiabatic coupling vectors. Equally, we probe the ability of the ground-to-excited state intersection ring exhibited by AA LR-TDDFT in protonated formaldimine to give rise to a similar topological phase in spite of its incorrect dimensionality.

Uncovering the Structural and Binding Insights of Dual Inhibitors Simultaneously Targeting Two Distinct Sites on EGFR Kinase

Epidermal growth factor receptor (EGFR) is the first growth factor receptor identified in normal cells that is related to the receptor tyrosine kinase, which causes regular cell division. A point mutation in EGFR intracellular kinase domain forces the abnormal cell divisions throughout time, leading to non-small cell lung cancer (NSCLC) transformation. Thus, competitive inhibitors that bind to the ATP binding pocket have been developed as a targeted therapy for NSCLC. The third-generation kinase inhibitor Osimertinib is currently playing a very vital role in the treatment of NSCLC. However, it is not effective toward the C797S kinase domain mutation. For this reason, fourth-generation kinase noncompetitive inhibitors are introduced which work through binding to an allosteric pocket near the ATP binding region and act as a better binding agent for this mutated kinase domain. However, the problem is that these single fourth-generation kinase inhibitors may not be as effective as a single agent. The aim of this work was to apply combinations of these two inhibitors together in different binding regions of EGFR without overlapping the resistance mechanism to obtain the key direct and indirect interactions occurring between them. Moreover, the free energy of dissociation of an inhibitor from its binding sites in the presence of a second inhibitor immobilized in another binding site was also the focus of the study. To realize this aim, we performed conventional molecular dynamics simulations and principal component analysis and dynamic cross-correlation matrices along with umbrella sampling. Our results demonstrated that binding of dual inhibitors triggered conformational changes of the protein more toward the inactive state. Furthermore, allosteric inhibitors bound more strongly to protein kinase EGFR than the orthosteric inhibitors in the presence of dual inhibitors. Finally, the binding mechanism and important hydrogen-bonding residues during unbinding of the inhibitors were fully elucidated. This study provides insight into the binding of the receptor-orthosteric inhibitor-allosteric inhibitor, which can be helpful for further design of novel inhibitors that have a better inhibitory action.

On the description of conical intersections between excited electronic states with LR-TDDFT and ADC(2)

Conical intersections constitute the conceptual bedrock of our working understanding of ultrafast, nonadiabatic processes within photochemistry (and photophysics). Accurate calculation of potential energy surfaces within the vicinity of conical intersections, however, still poses a serious challenge to many popular electronic structure methods. Multiple works have reported on the deficiency of methods like linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) or algebraic diagrammatic construction to second-order [ADC(2)]-approaches often used in excited-state molecular dynamics simulations-to describe conical intersections between the ground and excited electronic states. In the present study, we focus our attention on conical intersections between excited electronic states and probe the ability of AA LR-TDDFT and ADC(2) to describe their topology and topography, using protonated formaldimine and pyrazine as two exemplar molecules. We also take the opportunity to revisit the performance of these methods in describing conical intersections involving the ground electronic state in protonated formaldimine-highlighting in particular how the intersection ring exhibited by AA LR-TDDFT can be perceived either as a (near-to-linear) seam of intersection or two interpenetrating cones, depending on the magnitude of molecular distortions within the branching space.

Dimer Interface Destabilization of Photodissociative Dronpa Driven by Asymmetric Monomer Dynamics

Photoswitchable Dronpa (psDronpa) is a unique member of the fluorescent protein family that can undergo reversible photoinduced switching between fluorescent and dark states and has recently been engineered into a dimer (pdDronpaV) that can dissociate and reassociate as part of its photoswitchable pathway. However, the specific details of the protein structure-function relationship of the dimer interface along with how the dimer proteins interact with each other upon chromophore isomerization are not yet clear. Classical molecular dynamics simulations were performed on psDronpa as monomers and dimers as well as the pdDronpaV dimer and with cis/trans chromophore structures. Analysis of the cis and trans isomers of the chromophore illustrated key differences between their interactions with residues in the protein in both the monomer and dimer forms of psDronpa. Examination of the psDronpa dimer showed nonidentical chromophore interactions between the domains, indicating domain directional favoring. Examination of the trans form of pdDronpaV illuminated the importance of hydrogen bonding between the monomeric domains in maintaining their association, as well as illustrating the motion of dissociation of the domains. This discovery offers important information for possible future mutations of pdDronpaV that might be made to accelerate dissociation.

A glutamine-based single α-helix scaffold to target globular proteins

The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.

InteraChem: Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics

InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree-Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.

SSAIMS-Stochastic-Selection Ab Initio Multiple Spawning for Efficient Nonadiabatic Molecular Dynamics

Ab initio multiple spawning provides a powerful and accurate way of describing the excited-state dynamics of molecular systems, whose strength resides in the proper description of coherence effects during nonadiabatic processes thanks to the coupling of trajectory basis functions. However, the simultaneous propagation of a large number of trajectory basis functions can be numerically inconvenient. We propose here an elegant and simple solution to this issue, which consists of (i) detecting uncoupled groups of coupled trajectory basis functions and (ii) selecting stochastically one of these groups to continue the ab initio multiple spawning dynamics. We show that this procedure can reproduce the results of full ab initio multiple spawning dynamics in cases where the uncoupled groups of trajectory basis functions stay uncoupled throughout the dynamics (which is often the case in high-dimensional problems). We present and discuss the aforementioned idea in detail and provide simple numerical applications on indole, ethylene, and protonated formaldimine, highlighting the potential of stochastic-selection ab initio multiple spawning.

Stereoselectivity of Aldose Reductase in the Reduction of Glutathionyl-Hydroxynonanal Adduct

The formation of the adduct between the lipid peroxidation product 4-hydroxy-2-nonenal (HNE) and glutathione, which leads to the generation of 3-glutathionyl-4-hydroxynonane (GSHNE), is one of the main routes of HNE detoxification. The aldo-keto reductase AKR1B1 is involved in the reduction of the aldehydic group of both HNE and GSHNE. In the present study, the effect of chirality on the recognition by aldose reductase of HNE and GSHNE was evaluated. AKR1B1 discriminates very modestly between the two possible enantiomers of HNE as substrates. Conversely, a combined kinetic analysis of the glutathionyl adducts obtained starting from either 4R- or 4S-HNE and mass spectrometry analysis of GSHNE products obtained from racemic HNE revealed that AKR1B1 possesses a marked preference toward the 3S,4R-GSHNE diastereoisomer. Density functional theory and molecular modeling studies revealed that this diastereoisomer, besides having a higher tendency to be in an open aldehydic form (the one recognized by AKR1B1) in solution than other GSHNE diastereoisomers, is further stabilized in its open form by a specific interaction with the enzyme active site. The relevance of this stereospecificity to the final metabolic fate of GSHNE is discussed.

GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations

In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials.