An official website of the United States government
Proton transfer is crucial in various chemical and biological processes. Because of significant nuclear quantum effects, accurate and efficient description of proton transfer remains a great challenge. In this Communication, we apply constrained nuclear–electronic orbital density functional theory (CNEO-DFT) and constrained nuclear–electronic orbital molecular dynamics (CNEO-MD) to three prototypical shared proton systems and investigate their proton transfer modes. We find that with a good description of nuclear quantum effects, CNEO-DFT and CNEO-MD can well describe the geometries and vibrational spectra of the shared proton systems. Such a good performance is in significant contrast to DFT and DFT-based ab initio molecular dynamics, which often fail for shared proton systems. As an efficient method based on classical simulations, CNEO-MD is promising for future investigations of larger and more complex proton transfer systems.
more »
« less
Where is the hidden intramolecular H-bonding vibrational signal in the proline matrix IR spectrum?
The assignment of the hydrogen bonded O–H stretch vibration in the proline matrix IR spectrum has sparked controversy. Employing constrained nuclear electronic orbital methods, we provide a clear assignment that the vibrational frequency drops to near 3000 cm−1 as a result of the interplay between electronic effects, nuclear quantum effects, and matrix effects.
more »
« less
- Award ID(s):
- 2238473
- PAR ID:
- 10557622
- Publisher / Repository:
- American Institute of Physics
- Date Published:
- Journal Name:
- The Journal of Chemical Physics
- Volume:
- 161
- Issue:
- 13
- ISSN:
- 0021-9606
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Nuclear morphology plays a critical role in regulating gene expression and cell functions. While most research has focused on the direct effects of nuclear morphology on cell fate, its impact on the cell secretome and surrounding cells remains largely unexplored. In this study, we fabricate implants with a micropillar topography using methacrylated poly(octamethylene citrate)/hydroxyapatite (mPOC/HA) composites to investigate how micropillar-induced nuclear deformation influences cell secretome for osteogenesis and cranial bone regeneration. In vitro, cells with deformed nuclei show enhanced secretion of proteins that support extracellular matrix (ECM) organization, which promotes osteogenic differentiation in neighboring mesenchymal stromal cells (MSCs). In a female mouse model with critical-size cranial defects, nuclear-deformed MSCs on micropillar mPOC/HA implants elevate Col1a2 expression, contributing to bone matrix formation, and drive cell differentiation toward osteogenic progenitor cells. These findings indicate that micropillars modulate the secretome of hMSCs, thereby influencing the fate of surrounding cells through matricrine effects.more » « less
-
The hybrid quantum mechanics/molecular mechanics (QM/MM) approach, which combines the accuracy of QM methods with the efficiency of MM methods, is widely used in the study of complex systems. However, past QM/MM implementations often neglect or face challenges in addressing nuclear quantum effects, despite their crucial role in many key chemical and biological processes. Recently, our group developed the constrained nuclear-electronic orbital (CNEO) theory, a cost-efficient approach that accurately addresses nuclear quantum effects, especially quantum nuclear delocalization effects. In this work, we integrate CNEO with the QM/MM approach through the electrostatic embedding scheme and apply the resulting CNEO QM/MM to two hydrogen-bonded complexes. We find that both solvation effects and nuclear quantum effects significantly impact hydrogen bond structures and dynamics. Notably, in the glutamic acid–glutamate complex, which mimics a common low barrier hydrogen bond in biological systems, CNEO QM/MM accurately predicts nearly equal proton sharing between the two residues. With an accurate description of both quantum nuclear delocalization effects and environmental effects, CNEO QM/MM is a promising new approach for simulating complex chemical and biological systems.more » « less
-
We demonstrate that working with a correct phase-space electronic Hamiltonian captures electronic inertial effects. In particular, we show that phase space surface hopping dynamics do not suffer (at least to very high order) from non-physical non-adiabatic transitions between electronic eigenstates during the course of pure nuclear translational and rotational motion. This work opens up many new avenues for quantitatively investigating complex phenomena, including angular momentum transfer between chiral phonons and electrons as well as chiral-induced spin selectivity effects.more » « less
-
A new electronic transition is reported for the linear C 6 + cation with an origin at 416.8 nm. This spectrum can be compared to the matrix isolation spectra at lower energies reported previously by Fulara et al. [J. Chem. Phys. 123, 044305 (2005)], which assigned linear and cyclic isomers, and to the gas phase spectrum reported previously by Campbell and Dunk [Rev. Sci. Instrum. 90, 103101 (2019)], which detected the same cyclic-isomer spectrum reported by Fulara. Comparisons to electronically excited states and vibrations predicted by various forms of theory allow assignment of the spectrum to a new electronic state of linear C 6 + . The spectrum consists of a strong origin band, two vibronic progression members at higher energy and four hot bands at lower energies. The hot bands provide the first gas phase information on ground state vibrational frequencies. The vibrational and electronic structure of C 6 + provide a severe challenge to computational chemistry.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1063/5.0226184
