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Daniel Sucerquia

Publications and source records attributed to Daniel Sucerquia.

3 recordsLinked to original sources

SITH: A Quantum-Chemical Framework for Predicting Bond Destabilization in Stretched Molecules

Mechanical forces can selectively destabilize chemical bonds of molecular systems, particularly in biological and synthetic polymers. While experimental and theoretical methods have advanced our understanding of mechanochemical processes, predicting where energy concentrates within a molecule remains a significant challenge. To address this, we introduce SITH (Splitting Intramolecular Tension due to stretcHing), a novel method that decomposes the total electronic energy change of a stretched molecule into contributions from individual degrees of freedom -- such as bond lengths, angles, and dihedrals -- using numerical integration of the work-energy theorem. Unlike previous approaches that rely on harmonic approximations, SITH provides high accuracy and robustness to study the distribution of energies of stretched molecules up to a first bond cleavage. Although SITH uses 3N-6 degrees of freedom for the energy decomposition, we show that it can work even for ring structures like prolines. We apply SITH to a dataset of tripeptides and demonstrate that glycine and proline exhibit significantly different energy distributions in their Ca-C backbone bonds under tension: glycine stores more energy, making it more prone to rupture, while proline has the opposite behaviour. These findings reveal intrinsic differences in mechanochemical susceptibility across amino acids, offering more accurate predictions of bond rupture in proteins, and similarly in other (bio)polymers. SITH thus provides a powerful, interpretable tool for understanding energy distribution at the quantum level, with possible implications in mechanochemistry and force field validation.

physics.chem-ph

PLUMED Tutorials: a collaborative, community-driven learning ecosystem

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce ``PLUMED Tutorials'', a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

physics.ed-ph

Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters

Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes and enhanced-sampling algorithms and the ASE module, which includes several ab initio electronic structure codes. The interface is validated with a Lennard-Jones cluster free-energy landscape calculation by averaging multiple short metadynamics trajectories. We use this interface and analysis to estimate the free-energy landscape of Ag5 and Ag6 clusters at 10, 100 and 300 K with the radius of gyration and coordination number as collective variables, finding at most tens of meV in error. Relative free-energy differences between the planar and non-planar isomers of both clusters decrease with temperature, in agreement with previously proposed stabilization of non-planar isomers. Interestingly, we find that Ag6 is the smallest silver cluster where entropic effects at room temperature boost the non planar isomer probability to a competing state. The new ASE-PLUMED interface enables simulating nanosystem electronic properties at more realistic temperature-dependent conditions.

cond-mat.mtrl-sci