Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state

2017 ◽  
Vol 19 (34) ◽  
pp. 22969-22980 ◽  
Author(s):  
Oleg N. Starovoytov ◽  
Pengzhi Zhang ◽  
Piotr Cieplak ◽  
Margaret S. Cheung
Keyword(s):  
Force Field ◽  
Ground State ◽  
Energy Surface ◽  
Light Harvesting ◽  
Induced Polarization ◽  
Conformational Space ◽  
Chemical Bonds ◽  
Free Energy Surface ◽  
Polarizable Force Field ◽  
Conformational Distribution

Free energy surface of the light-harvesting triad employing a non-polarizable force field (NFF) and a polarizable force field (PFF) shows that induced polarization limits the motion of rotation about chemical bonds as well as bending at the porphyrin, which are prominent using the NFF, thus limiting the conformational space of the triad.

Testing and Optimizing the Drude Polarizable Force Field for Blocked Amino Acids Based on High-Level Quantum-Mechanical Energy Surfaces

2022 ◽  
pp. 1-9
Author(s):  
Jinfeng Chen ◽  
Gerhard König
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Energy Surface ◽  
Mechanical Energy ◽  
Quantum Mechanical ◽  
Polarizable Force Field ◽  
Conformational Substates ◽  
Reorganization Energies ◽  
High Level ◽  
Energy Surfaces

The correct reproduction of conformational substates of amino acids was tested for the CHARMM Drude polarizable force field. This was achieved by evaluating the reorganization energies for all low lying energy minima occurring in all 15 neutral blocked amino acids on a quantum-mechanical (QM) energy surface at the MP2/cc-pVDZ level. The results indicate that the bonded parameters of the N-acetyl (ACE) and N-Methylamide (CT3) blocking groups lead to significant discrepancies. A reparametrization of five bond angles significantly improved the agreement with the QM energy surface. The corrected Drude force field exhibits almost the same average reorganization energies relative to the MP2 energy surface as the AM1 and PM3 semi-empirical methods.

scholarly journals Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11− Fluxional Cluster

Materials ◽  
2020 ◽  
Vol 14 (1) ◽  
pp. 112
Author(s):  
Carlos Emiliano Buelna-Garcia ◽  
José Luis Cabellos ◽  
Jesus Manuel Quiroz-Castillo ◽  
Gerardo Martinez-Guajardo ◽  
Cesar Castillo-Quevedo ◽  
...  
Keyword(s):  
Free Energy ◽  
Infrared Spectrum ◽  
Infrared Spectra ◽  
Thermal Effects ◽  
Global Minimum ◽  
Energy Surface ◽  
Weighted Sums ◽  
Free Energy Surface ◽  
Temperature Dependent ◽  
Relative Population

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.

scholarly journals The Influence of Starch Origin on the Properties of Starch Films: Packaging Performance

Materials ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1146
Author(s):  
Zuzanna Żołek-Tryznowska ◽  
Alicja Kałuża
Keyword(s):  
Tensile Strength ◽  
Free Energy ◽  
Surface Free Energy ◽  
Food Packaging ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Casting Method ◽  
Starch Solution ◽  
Film Properties ◽  
Starch Films

Starch films can be used as materials for food packaging purposes. The goal of this study is to compare how the starch origin influence the selected starch film properties. The films were made from various starches such as that from maize, potato, oat, rice, and tapioca using 50%w of glycerine as a plasticizer. The obtained starch-based films were made using the well-known casting method from a starch solution in water. The properties of the films that were evaluated were tensile strength, water vapour transition rate, moisture content, wettability, and their surface free energy. Surface free energy (SFE) and its polar and dispersive components were calculated using the Owens-Wendt-Rabel-Kaelbe approach. The values of SFE in the range of 51.64 to 70.81 mJ∙m−2 for the oat starch-based film and the maize starch-based film. The films revealed worse mechanical properties than those of conventional plastics for packaging purposes. The results indicated that the poorest tensile strength was exhibited by the starch-based films made from oat (0.36 MPa) and tapioca (0.78 MPa) and the greatest tensile strength (1.49 MPa) from potato.

Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme

2015 ◽  
Vol 17 (40) ◽  
pp. 26955-26968 ◽  
Author(s):  
Toshio Asada ◽  
Kanta Ando ◽  
Koji Sakurai ◽  
Shiro Koseki ◽  
Masataka Nagaoka
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Efficient Approach ◽  
Reaction Processes ◽  
Dipole Response

An efficient approach to evaluate free energy gradients within the QM/MM framework has been proposed to clarify reaction processes on the free energy surface.

scholarly journals The role of ammonia in sulfuric acid ion induced nucleation

2008 ◽  
Vol 8 (11) ◽  
pp. 2859-2867 ◽  
Author(s):  
I. K. Ortega ◽  
T. Kurtén ◽  
H. Vehkamäki ◽  
M. Kulmala
Keyword(s):  
Sulfuric Acid ◽  
Quantum Chemical ◽  
Local Minimum ◽  
Good Accuracy ◽  
Energy Surface ◽  
Ground Level ◽  
Computational Effort ◽  
Free Energy Surface ◽  
Large Clusters

Abstract. We have developed a new multi-step strategy for quantum chemical calculations on atmospherically relevant cluster structures that makes calculation for large clusters affordable with a good accuracy-to-computational effort ratio. We have applied this strategy to evaluate the relevance of ternary ion induced nucleation; we have also performed calculations for neutral ternary nucleation for comparison. The results for neutral ternary nucleation agree with previous results, and confirm the important role of ammonia in enhancing the growth of sulfuric acid clusters. On the other hand, we have found that ammonia does not enhance the growth of ionic sulfuric acid clusters. The results also confirm that ion-induced nucleation is a barrierless process at high altitudes, but at ground level there exists a barrier due to the presence of a local minimum on the free energy surface.

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

1999 ◽  
Vol 110 (2) ◽  
pp. 741-754 ◽  
Author(s):  
Jay L. Banks ◽  
George A. Kaminski ◽  
Ruhong Zhou ◽  
Daniel T. Mainz ◽  
B. J. Berne ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Point Charge ◽  
Point Charge Model ◽  
Polarizable Force Field ◽  
Charge Model
Sign in / Sign up

Export Citation Format

Share Document