Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
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Adv Sci (Weinh)
January 2025
School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, China.
After cyclo-pentazolate anion, a 5/6 fused structure of N is constructed, and four novel nitrogen-rich ionic compounds are assembled on its basis. The results of the quantum calculations revealed an uneven distribution of electrons on cyclo-N , with significant charge density near the N5/N9 atoms and an ADCH charge of -0.425.
View Article and Find Full Text PDFActa Crystallogr B Struct Sci Cryst Eng Mater
February 2025
Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, United Kingdom.
We present an approach to reduce this computational cost substantially, based on the partitioning of the molecule into geometrically separated torsional groups, with the dependence of the intramolecular energy and atomic point charges and dependent degrees of freedom on molecular conformation being computed as a linear combination of the contributions of these groups. This can lead to large savings in computational cost without a significant impact on accuracy, as demonstrated in the cases of N-acetyl-para-aminophenol (paracetamol) and methyl 4-hydroxybenzoate (methyl paraben). The approach is also applied successfully to two larger molecules, benzyl [4-(4-methyl-5-[(4-methylphenyl)sulfonyl]-1,3-thiazol-2-yl)phenyl]carbamate (molecule XX from the fifth CSP blind test) and (2S)-2-[4-(3-fluorobenzyloxy)benzylamino]propionamide (safinamide), for which we conduct the first reported CSP study.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Physics Postgraduate Program, Institute of Physics, University of Brasília, 70910-900 Brasília-DF, Brazil.
Two-dimensional (2D) nanomaterials are at the forefront of potential technological advancements. Carbon-based materials have been extensively studied since synthesizing graphene, which revealed properties of great interest for novel applications across diverse scientific and technological domains. New carbon allotropes continue to be explored theoretically, with several successful synthesis processes for carbon-based materials recently achieved.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States.
Here we demonstrate how a biologically relevant molecule, riboflavin (vitamin B2), operates by a dual mode of action to effectively control crystallization of ammonium urate (NHHU), which is associated with cetacean kidney stones. In situ microfluidics and atomic force microscopy experiments confirm a strong interaction between riboflavin and NHHU crystal surfaces that substantially inhibits layer nucleation and spreading by kinetic mechanisms of step pinning and kink blocking. Riboflavin does not alter the distribution of tautomeric urate isomers, but its adsorption on NHHU crystal surfaces does interfere with the effects of minor urate tautomer by limiting its ability to induce NHHU crystal defects while also suppressing NHHU nucleation and inhibiting crystal growth by 80% at an uncharacteristically low modifier concentration.
View Article and Find Full Text PDFChemistry
January 2025
University of Sussex, Department of Chemistry, School of Life Sciences, BN1 9QJ, Brighton, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND.
The synthesis, structures and magnetic properties of an η5-silole complex and an η5-stannole complex of erbium are reported. The sandwich complex anions [(η5-CpSi)Er(η8-COT)]- and [(η5-CpSn)Er(η8-COT)]-, where CpSi is [SiC4-2,5-(SiMe3)2-3,4-Ph2]2- (1Si), CpSn is [SnC4-2,5-(SiMe3)2-3,4-Me2]2- (1Sn) and COT = cyclo-octatetraenyl, were obtained as their [K(2.2.
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