scholarly journals When Are Two Hydrogen Bonds Better than One? Accurate First-Principles Models Explain the Balance of Hydrogen Bond Donors and Acceptors Found in Proteins

2020 ◽  
Author(s):  
Vyshnavi Vennelakanti ◽  
Helena W. Qi ◽  
Rimsha Mehmood ◽  
Heather Kulik
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy Surfaces ◽  
Predictive Accuracy ◽  
Protein Structures ◽  
Geometric Constraints ◽  
Model Systems ◽  
Electronic Effects ◽  
Many Body ◽  
Wide Range ◽  
Energy Surfaces

<p>Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (i.e., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4,000 HBs, of which > 500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H···O HBs than N–H···O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction. </p>

scholarly journals When Are Two Hydrogen Bonds Better than One? Accurate First-Principles Models Explain the Balance of Hydrogen Bond Donors and Acceptors Found in Proteins

2020 ◽  
Author(s):  
Vyshnavi Vennelakanti ◽  
Helena W. Qi ◽  
Rimsha Mehmood ◽  
Heather Kulik
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy Surfaces ◽  
Predictive Accuracy ◽  
Protein Structures ◽  
Geometric Constraints ◽  
Model Systems ◽  
Electronic Effects ◽  
Many Body ◽  
Wide Range ◽  
Energy Surfaces

<p>Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (i.e., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4,000 HBs, of which > 500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H···O HBs than N–H···O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction. </p>

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

2020 ◽  
Author(s):  
Christian Devereux ◽  
Justin Smith ◽  
Kate Davis ◽  
Kipton Barros ◽  
Roman Zubatyuk ◽  
...  
Keyword(s):  
Drug Development ◽  
Autonomous Vehicles ◽  
Potential Energy Surfaces ◽  
Organic Molecules ◽  
Chemical Elements ◽  
Molecular Potential ◽  
Wide Range ◽  
Energy Surfaces ◽  
New Applications ◽  
Physical Phenomena

<p>Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, S) make up ~90% of drug like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~10<sup>6</sup> factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.</p>

Quenching rates and critical densities of c-C3H2

2019 ◽  
Vol 15 (S350) ◽  
pp. 148-151
Author(s):  
Malek Ben Khalifa ◽  
Emna Sahnoun ◽  
Silvia Spezzano ◽  
Laurent Wiesenfeld ◽  
Kamel Hammami ◽  
...  
Keyword(s):  
Potential Energy Surfaces ◽  
Full Potential ◽  
Thermodynamical Equilibrium ◽  
Medium Temperature ◽  
Permanent Electric Dipole Moment ◽  
Temperature Regimes ◽  
Wide Range ◽  
History Of ◽  
Energy Surfaces ◽  
Local Thermodynamical Equilibrium

AbstractCyclopropenylidene,, is a simple hydrocarbon, ubiquitous in astrophysical gases, and possessing a permanent electric dipole moment. Its readily observed multifrequency rotational transitions make it an excellent probe for the physics and history of interstellar matter. The collisional properties of with He are presented here. We computed the full Potential Energy Surfaces, and we perform quantum scattering in order to provide rates of quenching and excitation for low to medium temperature regimes. We discuss issues with the validity of the usual Local Thermodynamical Equilibrium assumption, and also the intricacies of the spectroscopy of an asymmetric top. We present the wide range of actual critical densities, as recently observed.

Global and local minima of protonated acetonitrile clusters

2020 ◽  
Vol 44 (40) ◽  
pp. 17558-17569 ◽  
Author(s):  
Alhadji Malloum ◽  
Jeanet Conradie
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Local Minima ◽  
Energy Surfaces ◽  
Global And Local

Potential energy surfaces of protonated acetonitrile clusters have been explored to locate global and local minima energy structures. The structures are stabilized by strong hydrogen bonds, anti-parallel dimers, dipole–dipole and CH⋯N interactions.

scholarly journals De novo exploration and self-guided learning of potential-energy surfaces

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Noam Bernstein ◽  
Gábor Csányi ◽  
Volker L. Deringer
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Materials Science ◽  
De Novo ◽  
Interatomic Potential ◽  
Single Point ◽  
Small Unit ◽  
Wide Range ◽  
Unit Cells ◽  
Energy Surfaces

Abstract Interatomic potential models based on machine learning (ML) are rapidly developing as tools for material simulations. However, because of their flexibility, they require large fitting databases that are normally created with substantial manual selection and tuning of reference configurations. Here, we show that ML potentials can be built in a largely automated fashion, exploring and fitting potential-energy surfaces from the beginning (de novo) within one and the same protocol. The key enabling step is the use of a configuration-averaged kernel metric that allows one to select the few most relevant and diverse structures at each step. The resulting potentials are accurate and robust for the wide range of configurations that occur during structure searching, despite only requiring a relatively small number of single-point DFT calculations on small unit cells. We apply the method to materials with diverse chemical nature and coordination environments, marking an important step toward the more routine application of ML potentials in physics, chemistry, and materials science.

scholarly journals Theoretical Studies of Dynamic Interactions in Excited States of Hydrogen-Bonded Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Marek J. Wójcik ◽  
Marek Boczar ◽  
Łukasz Boda
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy ◽  
Benzoic Acid ◽  
Excited States ◽  
Potential Energy Surfaces ◽  
Low Frequency ◽  
Fermi Resonance ◽  
Tunneling Splittings ◽  
Energy Surfaces ◽  
Hydrogen Bonded

Theoretical model for vibrational interactions in the hydrogen-bonded benzoic acid dimer is presented. The model takes into account anharmonic-type couplings between the high-frequency O–H and the low-frequency O⋯O stretching vibrations in two hydrogen bonds, resonance interactions between two hydrogen bonds in the dimer, and Fermi resonance between the O–H stretching fundamental and the first overtone of the O–H in-plane bending vibrations. The model is used for theoretical simulation of the O–H stretching IR absorption bands of benzoic acid dimers in the gas phase in the first excited singlet state. Ab initio CIS and CIS(D)/CIS/6-311++G(d,p) calculations have been carried out in the à state of tropolone. The grids of potential energy surfaces along the coordinates of the tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials have been fitted to the calculated potential energy surfaces. The tunneling splittings for vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces give good estimation of the tunneling splittings in the vibrationally ground and excited states of tropolone, and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase of the tunneling splittings with the excitation of low-frequency planar modes.

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