An extrapolation method for the efficient calculation of molecular response properties within Born-Oppenheimer molecular dynamics

The calculation of molecular response properties in dynamic molecular systems is a major challenge that requires sampling over many steps of, e. g., Born-Oppenheimer molecular dynamics (BO-MD) simulations. We present an extrapolation scheme to accelerate such calculations for multiple steps within BO-MD trajectories or equivalently within other sampling methods of conformational space. The extrapolation scheme is related to the one introduced by Pulay and Fogarasi Chem. Phys. Lett., 2004, 386, 272] for self-consistent field (SCF) energy calculations. We extend the extrapolation to the quantities within our density matrix-based Laplace-transformed coupled perturbed SCF (DL-CPSCF) method that allows for linear-scaling calculations of response properties for large molecular systems. Here, we focus on the example of calculating NMR chemical shifts for which the number of required DL-CPSCF iterations reduces by roughly 40-70%

A Base-Independent Repair Mechanism for DNA Glycosylase-No Discrimination Within the Active Site

The ubiquitous occurrence of DNA damages renders its repair machinery a crucial requirement for the genomic stability and the survival of living organisms. Deficiencies in DNA repair can lead to carcinogenesis, Alzheimer, or Diabetes II, where increased amounts of oxidized DNA bases have been found in patients. Despite the highest mutation frequency among oxidized DNA bases, the base-excision repair process of oxidized and ring-opened guanine, FapydG (2, 6-diamino-4-hydroxy-5-formamidopyrimidine),remained unclear since it is difficult to study experimentally. We use newly-developed linear-scaling quantum-chemical methods (QM) allowing us to include up to 700 QM-atoms and achieving size convergence. Instead of the widely assumed base-protonated pathway we find a ribose-protonated repair mechanism which explains experimental observations and shows strong evidence for a base-independent repair process. Our results also imply that discrimination must occur during recognition, prior to the binding within the active site

A Base-Independent Repair Mechanism for DNA Glycosylase-No Discrimination Within the Active Site

The ubiquitous occurrence of DNA damages renders its repair machinery a crucial requirement for the genomic stability and the survival of living organisms. Deficiencies in DNA repair can lead to carcinogenesis, Alzheimer, or Diabetes II, where increased amounts of oxidized DNA bases have been found in patients. Despite the highest mutation frequency among oxidized DNA bases, the base-excision repair process of oxidized and ring-opened guanine, FapydG (2, 6-diamino-4-hydroxy-5-formamidopyrimidine),remained unclear since it is difficult to study experimentally. We use newly-developed linear-scaling quantum-chemical methods (QM) allowing us to include up to 700 QM-atoms and achieving size convergence. Instead of the widely assumed base-protonated pathway we find a ribose-protonated repair mechanism which explains experimental observations and shows strong evidence for a base-independent repair process. Our results also imply that discrimination must occur during recognition, prior to the binding within the active site

Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics

Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We employ (1) the simplified TDDFT schemes of Grimme et al. and (2) the Hammes-Schiffer−Tully approach to obtain nonadiabatic couplings from finite-difference calculations. The resulting scheme delivers an accurate physical picture while virtually eliminating the two computationally most demanding steps of the algorithm. Combined with our GPU-based integral routines for SCF, TDDFT, and TDDFT derivative calculations, NAMD simulations of systems of a few hundreds of atoms at a reasonable time scale become accessible on a single compute node. To demonstrate this and to present a first, illustrative example, we perform TDDFT/MM-NAMD simulations of the rhodopsin protein

Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors

Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S1 lifetimes. Although all four rotors show different S1 excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies

H-2 Evolution with Covalent Organic Framework Photocatalysts

Covalent organic frameworks (COFs) are a new class of crystalline organic polymers that have garnered significant recent attention as highly promising H-2 evolution photocatalysts. This Perspective discusses the advances in this field of energy research while highlighting the underlying peremptory factors for the rational design of readily tunable COF photoabsorber-cocatalyst systems for optimal photo catalytic performance

From free-energy profiles to activation free energies

Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) discriminating between R and P, we define the free-energy profile (FEP) as the logarithm of the marginal Boltzmann distribution of the CV. This FEP is not a true free energy. Nevertheless, it is common to treat the FEP as the “free-energy” analog of the minimum potential energy path and to take the activation free energy, ΔF‡ RP, as the difference between the maximum at the transition state and the minimum at R. We show that this approximation can result in large errors. The FEP depends on the CV and is, therefore, not unique. For the same reaction, different discriminating CVs can yield different ΔF‡ RP. We derive an exact expression for the activation free energy that avoids this ambiguity. We find ΔF‡ RP to be a combination of the probability of the system being in the reactant state, the probability density on the dividing surface, and the thermal de Broglie wavelength associated with the transition. We apply our formalism to simple analytic models and realistic chemical systems and show that the FEP-based approximation applies only at low temperatures for CVs with a small effective mass. Most chemical reactions occur on complex, high-dimensional PES that cannot be treated analytically and pose the added challenge of choosing a good CV. We study the influence of that choice and find that, while the reaction free energy is largely unaffected, ΔF‡ RP is quite sensitive

Ionothermal Synthesis of Imide‐Linked Covalent Organic Frameworks

Covalent organic frameworks (COFs) are an extensively studied class of porous materials, which distinguish themselves from other porous polymers in their crystallinity and high degree of modularity, enabling a wide range of applications. COFs are most commonly synthesized solvothermally, which is often a time‐consuming process and restricted to well‐soluble precursor molecules. Synthesis of polyimide‐linked COFs (PI‐COFs) is further complicated by the poor reversibility of the ring‐closing reaction under solvothermal conditions. Herein, we report the ionothermal synthesis of crystalline and porous PI‐COFs in zinc chloride and eutectic salt mixtures. This synthesis does not require soluble precursors and the reaction time is significantly reduced as compared to standard solvothermal synthesis methods. In addition to applying the synthesis to previously reported imide COFs, a new perylene‐based COF was also synthesized, which could not be obtained by the classical solvothermal route. In situ high‐temperature XRPD analysis hints to the formation of precursor–salt adducts as crystalline intermediates, which then react with each other to form the COF

Single-Site Photocatalytic H-2 Evolution from Covalent Organic Frameworks with Molecular Cobaloxime Co-Catalysts

We demonstrate photocatalytic hydrogen evolution using COF photosensitizers with molecular proton reduction catalysts for the first time. With azine-linked N2-COF photosensitizer, chloro(pyridine)cobaloxime co-catalyst, and TEOA donor, H-2 evolution rate of 782,mu mol h(-1) g(-1) and TON of 54.4 has been obtained in a water/acetonitrile mixture. PXRD, solid-state spectroscopy, EM analysis, and quantum-chemical calculations suggest an outer sphere electron transfer from the COF to the co-catalyst which subsequently follows a monometallic pathway of H-2 generation from the Co-III-hydride and/or Co-II-hydride species