Article
Forestry
Kengo Shigetomi, Mana Tokizawa, Yasumitsu Uraki
Summary: By preparing highly deuterated monolignols, a facile methodology for elucidating the lignin chain-growth mechanism was established. This study demonstrated that highly deuterated monolignols can effectively suppress NMR signals and serve as a unique molecular tool to differentiate signals of interest.
JOURNAL OF WOOD SCIENCE
(2022)
Article
Energy & Fuels
Fengxia Yue, Wu Lan, Liming Zhang, Fachuang Lu, Runcang Sun, John Ralph
Summary: A facile and efficient synthetic approach for higher-yield pinoresinol production was developed, impacting pinoresinol-related research and clinical applications.
FRONTIERS IN ENERGY RESEARCH
(2021)
Article
Chemistry, Physical
Thien T. Nguyen, Phong Q. Le, Jussi Helminen, Jussi Sipila
Summary: The study focused on calculating the H-1 and C-13 NMR chemical shifts of three lignin dimers, revealing that the omega B97XD functional consistently provided accurate results.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Mendel L. Perkins, Mathias Schuetz, Faride Unda, Kent T. Chen, Marcel B. Bally, Jayesh A. Kulkarni, Yifan Yan, Joana Pico, Simone Diego Castellarin, Shawn D. Mansfield, A. Lacey Samuels
Summary: The lignin polymerizing laccase enzymes in cell walls establish a concentration gradient that drives the diffusion of lignin monomers. The presence of laccases on one side of the membrane facilitates the diffusion of monolignols. This finding provides insights into the transport mechanism of monolignols and the role of cell wall oxidative enzymes in lignin biosynthesis.
Article
Chemistry, Physical
V. E. Petrenko, T. Bogdan, E. G. Odintsova, M. L. Antipova, V. Bogdan
Summary: In this study, the structures of two radical forms of coniferyl alcohol and their dimer were optimized using density functional means. Analysis of geometric parameters, interaction energies, and molecular electrostatic potential were conducted, revealing the energy preference for the formation of beta-O-4' bonds during the radical dimerization process, leading to the production of lignin.
RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Forestry
Lucas Lagerquist, Jani Rahkila, Patrik Eklund
Summary: A series of 6-substituted syringyl model compounds with various substituents were prepared and analyzed, showing a characteristic increase in C-13 NMR chemical shift of the methoxy group vicinal to the substitution. This peak could potentially be used to identify 6-condensation in syringylic lignin samples.
Article
Chemistry, Multidisciplinary
Takao Kishimoto, Ayumi Hiyama, Hiroshi Toda, Daisuke Urabe
Summary: This study investigated the differences in enzymatic polymerization of monolignols in two laccase systems. The highest enzyme activity of LacT was observed at pH 4, while that of LacR was highest at pH 7. Only CA was able to produce a dehydrogenation polymer (DHP) in both laccase systems, although SA was consumed at a higher rate. H-1-C-13 HSQC NMR analysis revealed the presence of lignin substructures in the DHPs obtained using LacT and LacR. The pH of the reaction solution was found to have a greater impact on the chemical structure of DHP than the source of laccases.
Article
Biochemistry & Molecular Biology
Yingying Yang, Jingyu Xu, Yue Kong, Jinghui Zhou, Xing Wang
Summary: A novel binary solvent system consisting of alcohols and dichloromethane was developed for efficiently dissolving various types of lignin. Adjusting the volume ratio of alcohol and dichloromethane significantly affected the solubility of lignin. The solvent can dissolve lignin due to the solvation of the hydrophobic skeleton by dichloromethane and the solvation of hydrophilic groups by alcohols, promoting the dissolution of lignin. The proposed solvent is simple, efficient, versatile, and flexible, with broad application prospects.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Thomas Elder, Jose C. del Rio, John Ralph, Jorge Rencoret, Hoon Kim
Summary: Diferuloylputrescine has been found to covalently bond with lignin, and this study provides evidence that it can be incorporated into the lignin polymer without thermodynamic impediment. The calculations show that both homo-coupling and cross-coupling reactions of Diferuloylputrescine are energetically favorable. This suggests that Diferuloylputrescine can be considered as a non-canonical lignin monomer.
Article
Chemistry, Multidisciplinary
Yasemin Yesiltepe, Niranjan Govind, Thomas O. Metz, Ryan S. Renslow
Summary: The majority of primary and secondary metabolites in nature have yet to be identified, posing a major challenge for metabolomics studies. Complete chemical characterization of metabolomes is currently infeasible due to technical and economic limitations. Computationally predicted data can be a viable solution to expand metabolite reference libraries, but accuracy is crucial. A study using simulated experimental and theoretical NMR chemical shift databases found that a certain level of accuracy is required for confident identification of metabolites in different samples.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Chemistry, Physical
Gregory K. Pierens
Summary: The calculation of DFT chemical shifts is crucial for verifying proposed structures, with the CCSI serving as a metric to measure deviations between calculated and experimental chemical shifts. While MAD is commonly used as a goodness of fit metric, it may mask large deviations in the data. A classification strategy for CCSI is also proposed to indicate when further evaluation of NMR data is needed.
Article
Chemistry, Physical
Xuhai Zhu, Bardo Bruijnaers, Tainise V. Lourencon, Mikhail Balakshin
Summary: Global carbon emission reduction goals have led to the development of biomass-based resins to replace petroleum-based products. The structural elucidation of softwood kraft lignin-based furfuryl alcohol resin revealed a high diversity of linkages and the formation of new condensed structures. The resin was produced through crosslinking between lignin fragments and furfuryl alcohol chains, with potential esterification reactions and aryl ethers formation.
Review
Chemistry, Multidisciplinary
Seth Beck, Phillip Choi, Samir H. Mushrif
Summary: This Review provides an overview of the state-of-the-art research on the microstructure of native biomass, including the linkages among individual biopolymers and the importance of quantifying biomass microstructure in developing mild, commercially viable, and carbon efficient deconstruction technologies.
REACTION CHEMISTRY & ENGINEERING
(2022)
Article
Biochemical Research Methods
Roy Hoffman
Summary: The study found that the chemical shift of TMS is influenced by solvent and environmental conditions. Therefore, methods for improving measurements were developed, and comparisons of chemical shifts in different solvents were made, showing the effects of polarizability and aromaticity on TMS chemical shift.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Chemistry, Multidisciplinary
Colleen L. Ray, James A. Gawenis, Charles Michael Greenlief
Summary: Nuclear magnetic resonance (NMR)-based screening of materials is a powerful tool for quality control, authenticity testing, and purity testing of compounds. However, reliance on specific reference compounds for spectral alignment may be inaccurate due to the formation of inclusion complexes, requiring vigilance and improved referencing techniques for accurate results.
MAGNETIC RESONANCE IN CHEMISTRY
(2022)
Article
Materials Science, Paper & Wood
Abhishek Singh, Albert L. Kwansa, Ho Shin Kim, Justin T. Williams, Hui Yang, Nan K. Li, James D. Kubicki, Alison W. Roberts, Candace H. Haigler, Yaroslava G. Yingling
Article
Chemistry, Physical
Tsutomu Ohno, James D. Kubicki
JOURNAL OF PHYSICAL CHEMISTRY A
(2020)
Article
Chemistry, Multidisciplinary
Sara Soldoozy, Anthony Trinh, James D. Kubicki, Hind A. Al-Abadleh
Article
Geochemistry & Geophysics
Jason D. Boettger, James D. Kubicki
Summary: The formation of H2CO3 and HCO3 from CO2 in aqueous systems, through hydration and hydroxylation reactions, plays an important role in CaCO3 mineral precipitation and impacts paleoclimate proxy records. Quantum mechanical calculations of dissolved inorganic carbon species help predict kinetic isotope fractionations, with factors such as hydrogen bonds and C(CO2)-O(H2O or OH-) distances influencing the calculated values. The results suggest that regressing molecular model fractionation results against hydrogen bond patterns is a promising way to improve isotope fractionation calculations in aqueous systems.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2021)
Article
Chemistry, Physical
Ke Yuan, Nikhil Rampal, Paul Fenter, James D. Kubicki, Andrew G. Stack, Stephan Irle
Summary: The researchers used density functional tight-binding (DFTB) to simulate the structures of quartz surfaces with different types and densities of defects in water, revealing that the rotation of surface [SiO4] tetrahedra near Si vacancies can lead to outward displacements of Si atoms and inward relaxations of terminal oxygens.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Soil Science
Tsutomu Ohno, James D. Kubicki, Aria Amirbahman
Summary: Formation of mineral-associated organic matter contributes to soil carbon storage, but changing climate may destabilize minerals. Using model soil ligands, this study examines the chemical bonds formed between Fe cations and organic acids, providing insights into the biogeochemical cycling of soil Fe and C.
SOIL SCIENCE SOCIETY OF AMERICA JOURNAL
(2022)
Article
Environmental Sciences
Y. Ravi Kumar, Kalim Deshmukh, M. Mohamed Naseer Ali, Gade Abhijay, Wedad A. Al-Onazi, Amal M. Al-Mohaimeed, S. K. Khadheer Pasha
Summary: In this study, polyvinyl alcohol nanocomposite films reinforced with nickel oxide nanoparticles and graphene quantum dots were prepared and characterized. The resulting films showed good mechanical flexibility and improved tensile strength. Density functional theory calculations revealed that the PVA model indirectly interacts with GQDs through the NiO model, providing insight into the fundamental interactions within the nanocomposite film.
ENVIRONMENTAL RESEARCH
(2022)
Article
Chemistry, Physical
S. G. Mohammed Hussain, R. Kumar, M. Mohamed Naseer Ali, D. Sankar, V Kannappan
Summary: Ultrasonic study of binary liquid mixtures containing n-propyl amine and four different ethers shows the presence of H-bonded interactions and the influence of non-covalent interactions on molecular arrangement, with stronger H-bonded interactions in aromatic ethers systems. Optimized molecular geometries were obtained using Density Functional Theory (DFT) method.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
I. Salim Meeran, T. William Raja, V. N. Azger Dusthakeer, M. Mohamed Naseer Ali, S. Syed Tajudeen, T. K. Shabeer
Summary: A new series of isoniazid-Schiff base ligands and their metal complexes were synthesized and characterized. The Ni(ii) complex showed an ESR spectrum at room temperature, which is rare for non-Krammer systems. Docking studies revealed favorable binding interactions between the ligands and the MountKasB protein of Mycobacterium tuberculosis. Some complexes exhibited complete killing of the tuberculosis strain and could be potential metal-based anti-TB drugs.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Physical
Heath D. Watts, James D. Kubicki, Nadine Kabengi
Summary: Periodic plane-wave density functional theory calculations were conducted to model the exchange of Li+ with Na+, K+, or Rb+ on the alpha-quartz (SiO2) (101) surface. The calculated heats of exchange showed a consistent trend with experimental results, but the magnitude was significantly higher in the calculations. Possible reasons for this discrepancy were discussed.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Jason D. Boettger, Cajetan Neubauer, Sebastian H. Kopf, James D. Kubicki
Summary: The study of isotopic fingerprints in nitrate has provided important insights into the global nitrogen cycle and uncovered new knowledge gaps. Measuring the populations of isotopic homologs of intact NO3- ions shows promise for advancing the understanding of nitrogen cycling processes. The research also found that the isotopic composition of residual nitrate is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase.
ACS EARTH AND SPACE CHEMISTRY
(2022)
Review
Chemistry, Analytical
Hind A. Al-Abadleh, James D. Kubicki, Nicholas Meskhidze
Summary: With the increasing recognition of the need for interdisciplinary communication in addressing research questions related to climate change and pollution, this article focuses on the chemical reactivity of Fe-containing minerals in air, water, and the air-sea interface. The reactions driven by Fe have significant impacts on respiratory organs and aerosol properties, and the deposition of aerosol particles affects ocean biogeochemical processes. Enhancing the predictive power of atmospheric and ocean models is emphasized.
ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS
(2023)
Article
Multidisciplinary Sciences
Joshua T. Del Mundo, Sintu Rongpipi, Hui Yang, Dan Ye, Sarah N. Kiemle, Stephanie L. Moffitt, Charles L. Troxel, Michael F. Toney, Chenhui Zhu, James D. Kubicki, Daniel J. Cosgrove, Esther W. Gomez, Enrique D. Gomez
Summary: In this study, grazing-incidence wide-angle X-ray scattering (GIWAXS) with a humidity chamber was used to investigate the properties of onion cell walls. The results showed that the lattice spacing of cellulose (110/110) slightly decreased upon drying, while the lattice parameters of (200) remained unchanged. The intensity of (110/110) diffraction increased relative to (200) in hydrated samples. Density functional theory models confirmed the changes in crystalline properties during drying. GIWAXS also revealed a peak attributed to pectin chain aggregation.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Alireza Namayandeh, Olaf J. Borkiewicz, Nefeli M. Bompoti, Steven K. Watson, James D. Kubicki, Maria Chrysochoou, F. Marc Michel
Summary: This study used synchrotron scattering methods and chemical analysis to investigate the impact of oxyanion surface loading on the transformation of Fh. The results showed that adsorption of oxyanions decreased the transformation rate and favored the formation of Hm over Gt. The inhibitory effect of PO43- surface loading on Fh transformation was greater.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Chemistry, Physical
Izaac Sit, Mark A. Young, James D. Kubicki, Vicki H. Grassian
Summary: This study investigates the surface chemistry of nucleotides adsorbed on two different minerals, hematite and goethite, using infrared spectroscopy and density functional theory (DFT) calculations. The results show preferential adsorption of the phosphate group to either surface. The experimental absorption frequencies were compared to DFT calculations, revealing differences in the binding modes of nucleotides to the two mineral surfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)