Publications

Tianbiao Liu, Wenda Wu, Jian Luo, Fang Wang, Bing Yuan. Aqueous organic redox flow batteries (AORFBs) have become increasing attractive for scalable energy storage. However, it remains challenging to develop high voltage, powerful AORFBs because of the

Alexander I. Boldyrev, Nikolay V. Tkachenko. This research reports a search for peculiar monobridged structures of the E2H2 molecules (E = Be, Mg, Ca, Sr, Ba). For Be2H2 and Mg2H2, the monobridged geometry is not an equilibrium but rather a transition s

Cheng-Wei T. Chang, Yagya P. Subedi, Paul Roberts, Heath Montgomery, Noah Thakeray. Gap junction channels formed by the association of connexin hemichannels play a crucial role in intercellular communication. Connexin 43 (Cx43) is expressed in a variety

Alexander I. Boldyrev, Ivan Popov, Nikolay V. Tkachenko. In this work, the largest heterometallic supertetrahedral clusters, [Zn6Ge16]4– and [Cd6Ge16]4–, were directly self‐assembled through highly‐charged [Ge4]4– units and transition metal cations, in

Steve Scheiner. The various sorts of complexes in which HArF and AuX (X = F, Cl, Br, I) can engage are probed by MP2/aug‐cc‐pVTZ calculations. The most weakly bound are those containing a halogen bond (XB) of the AuX⋯FArH sort, with binding energies less...

Steve Scheiner. A central pnicogen Z atom (Z = Sb, As) is covalently attached to the O atom of three −O(CH2)nX chains where X represents either an aldehyde or amine group. The chain can fold around so that the basic X group can engage in a noncovalent p

Steve Scheiner. The complexation process between anionic ZCl4– (Z = P, As, Sb) and neutral NCH and pyridine, as well as the CN– anion, is studied in both the gas phase and aqueous solution by high-level ab initio calculations. Despite the absence of a p

Lisa M. Berreau, Josiah G. D. Elsberg. Interest in O2-dependent aliphatic carbon–carbon (C–C) bond cleavage reactions of first row divalent metal diketonate complexes stems from the desire to further understand the reaction pathways of enzymes such as D

Kimberly J. Hageman. Over the last 5 Million years, outstanding warm interglacial periods (i.e. 'super-interglacials') occurred under low atmospheric CO2 levels that may feature extensive Antarctica ice sheet collapse. Here, we focus on the extreme supe

Alvan C. Hengge. Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate

Alexander I. Boldyrev, Nikita Fedik, Ivan Popov. Until now, all B≡B triple bonds have been achieved by adopting two ligands in the L→B≡B←L manner. Herein, we report an alternative route of designing the B≡B bonds based on the assumption that by acquirin

Alexander I. Boldyrev, Nikolay V. Tkachenko. The structure and properties of two‐dimensional phosphoborane sheets were computationally investigated using Density Functional Theory calculations. The calculated phonon spectrum and band structure point to

Alexander I. Boldyrev, Maksim Kulichenko. Molybdenum disulfide is a prominent semiconductor that received a lot of attention recently due to its unique properties. Possessing a layered crystal structure, one can tune the band gap from indirect to direct

Yi Rao, Gang-Hua Deng, Yuqin Qian, Qianshun Wei, Tong Zhang. High even-order surface/interface specific spectroscopy has the potential to provide more structural and dynamical information about surfaces and interfaces. In this work, we developed a novel

Cheng-Wei T. Chang, Yagya P. Subedi, Madher N. AlFindee. Connexins hemichannels (HCs) from adjacent cells form gap-junctional channels that mediate cell-to-cell communication. Abnormal opening of “free” undocked HCs can produce cell damage and particip

Steve Scheiner. : A TrF2 group (Tr = B, Al, Ga, In, Tl) is placed on one of the α positions of naphthalene, and its ability to engage in a triel bond (TrB) with a weak (NCH) and strong (NC−) nucleophile is assessed by ab initio calculations. As a competi...

Nicholas E. Dickenson, Heather B. Case. Type three secretion systems (T3SS) are complex nano-machines that evolved to inject bacterial effector proteins directly into the cytoplasm of eukaryotic cells. Many high-priority human pathogens rely on one or m

Joan M. Hevel, Owen M. Price. Protein arginine methylation is a widespread eukaryotic posttranslational modification that occurs with as much frequency as ubiquitinylation. Yet how the nine different human protein arginine methyltransferases (PRMTs) reco...

Alexander I. Boldyrev, Maksim Kulichenko, Nikita Fedik. Single-atom catalysis is the ultimate approach in catalysis science which implies the utilization of a catalyst is as efficient as it gets. In this paper we suggest a new type of a single-atom (or

Steve Scheiner. The correct balance between hydrophobic London dispersion (LD) and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors we sought a comparison of the influenza

Alexander I. Boldyrev. The DFT calculations of the electronic structure, energy characteristic and spin densities of cobalt(II) diketonate adducts with polycyclic triangular hydrocarbons functionalized with o-benzoquinone groups aimed at search for spin

Kimberly J. Hageman, Sean M. Lyons. The Pesticide Loss via Volatilization model was developed to predict and understand pesticide volatilization rates from a planted agricultural field. The model allows the user to adjust the properties of the pesticide

Ryan N. Jackson, Valerie M. Crowley, Hannah N. Taylor, Josie Metcalf. Bacteria and archaea use CRISPR-Cas adaptive immune systems to destroy complementary nucleic acids using RNAs derived from CRISPR loci. Here, we provide the first functional evidence

Steve Scheiner. Research on σ-hole interactions that include halogen, chalcogen, pnicogen, and tetrel bonding has been accelerating in recent years. These cousins of the H-bond have many similar properties, including geometric preferences and energetics

Steve Scheiner. A computational study of the complexes formed by TF3OH (T=C, Si, Ge) with three nitrogen‐containing bases NCH, NH3, and imidazole (IM) is carried out at the MP2/aug‐cc‐pVTZ level. TF3OH can participate in two different types of noncovale

Kimberly J. Hageman. Over the last 5 million years, the Earth’s climate has oscillated between warm (interglacial) and cold (glacial) states. Some particularly warm interglacial periods (i.e. ‘super-interglacials’) occurred under low atmospheric CO2 and

Lance C. Seefeldt. The dark-operative protochlorophyllide oxidoreductase (DPOR) enzyme contains two [4Fe-4S]- containing component proteins (BchL and BchNB) that assemble in an ATP-dependent fashion to coordinate electron transfer and reduction of proto

Cheng-Wei Tom Chang, Uddav Pandey, Yagya Prasad Subedi, Madher N. Alfindee, Taylor Shepherd. 3- and 6-aminosugars are common motifs in bioactive compounds playing pivotal roles in the bioactivity of the core molecules to which they are attached. Howev

Alexander I. Boldyrev. Nikolay V. Tkachenko. Since the discovery of graphene, 2D materials have captured the minds of scientists because of their attractive and unique electronic properties. In particular, magnetic 2D materials have become a subjec

Joan M. Hevel. Owen M. Price. Protein arginine methylation is a widespread eukaryotic posttranslational modification that occurs to both histone and non-histone proteins. The S-adenosyl-L-methionine (AdoMet or SAM)-dependent modification is catalyzed by t...

Lisa M. Berreau, Tatiana Soboleva, Casey R. Simons Carbon monoxide (CO) is a gasotransmitter produced in humans. An essential unanswered question in the design of carbon monoxide releasing molecules (CORMs) is whether the delivery molecule should be lo

Lance C. Seefeldt. Nitrogenase is activated for N2 reduction through the accumulation of four reducing equivalents at the active-site FeMo-cofactor (FeMo-co: Fe7S9MoC; homocitrate) to form the key Janus intermediate, denoted E4(4H), whose lowest-energy

Gang Li. Enamines and enol ethers are versatile synthons for chemical synthesis. While several methods have been developed to access such molecules, prefunctionalized starting materials are usually required and direct desaturation methods remain rare. Her...

Steve Scheiner. The ability of two NH3 ligands to engage in simultaneous chalcogen bonds to a hypervalent YF4 molecule, with Y = S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis struc

Casey R. Simons. This report describes the implementation of a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dye into the ligand framework of a Rh-based catalyst. The redox-active nature of the BODIPY dye is utilized to generate a catalyst that is

Cheng-Wei Tom Chang, Yagya Prasad Subedi, Uddav Pandey, Madher N. Alfindee Amphiphilic kanamycins bearing hydrophobic modifications at the 6″ position have attracted interest due to remarkable antibacterial-to-antifungal switches in bioactivity. In this

Alexander I. Boldyrev, Nikolay V. Tkachenko, Nikita Fedik. Among the diversity of new materials, two-dimensional crystal structures have been attracting significant attention from the broad scientific community due to their promising applications in na

Scott A. Ensign, Lance C. Seefeldt, Mathangi Soundararajan A promising approach for the synthesis of high value reduced compounds is to couple bacteria to the cathode of an electrochemical cell, with delivery of electrons from the electrode driving red

T. Leo Liu, Kevin V. Nielson, Liping Zhang. Metal organic frameworks (MOFs) of the type NBu4M(DHBQ)1.5 (M = Ni2+, Fe2+, and Co2+; DHBQ = 2,5- dihydroxy-1,4-benzoquinone) were prepared with improved yield up to 100% via a simple benchtop aqueous additio

T. Leo Liu, Maowei Hu, Bo Hu, Jian Luo. Redox-active anthraquinone molecules represent promising anolyte materials in aqueous organic redox flow batteries (AORFBs). However, the chemical stability issue and corrosion nature of anthraquinone-based anoly

Kimberly J. Hageman, Robert E. Alumbaugh, Sean M. Lyons. Neonicotinoid insecticides have been shown to have high chronic toxicity relative to acute toxicity, and therefore short‐term toxicity tests ≤96 h in duration may underestimate their environmental

Steve Scheiner. Ongoing studies of the hydrogen bond (HB), in which a hydrogen (H) atom acts as a bridge between a pair of chemical groups, continues to offer new ideas about this interaction that have applications to biochemical processes. The ability

Kimberly J. Hageman. New Zealand uses more than a ton of pesticides each year; many of these are mobile, relatively persistent, and can make their way into waterways. While considerable effort goes into monitoring nutrients in agricultural streams and

Yi Rao, Yuqin Qian. Among the world’s most deadly toxins are a class of organophosphates that are used as chemical warfare agents (CWAs). It is imperative to continue to develop novel means for mitigation and protection against these chemical threats.

Joan M. Hevel Background: Creating designer molecules using a combination of select domains from polyketide synthases and/ or nonribosomal peptide synthetases (NRPS) continues to be a synthetic goal. However, an incomplete understanding of how protein-pro...

Lance C. Seefeldt, Derek F. Harris, Hayden Kallas, Zhi-Yong Yang. Three genetically distinct, but structurally similar, isozymes of nitrogenase catalyze biological N2 reduction to 2NH3: Mo-, V-, and Fe-nitrogenase, named respectively for the metal (M) i

Yi Rao, Yuqin Qian, Gang-hua Deng, Jordan Lapp. The growth of aerosol particles is intimately related to chemical reactions in the gas phase and particle phase and at gas−aerosol particle interfaces. While chemical reactions in gas and particle phases a

Kimberly Hageman. Environmental challenges persist across the world, including the Australasian region of Oceania, where biodiversity hotspots and unique ecosystems such as the Great Barrier Reef are common. These systems are routinely affected by mult

Yi Rao, Yujie Sun, Fuzhan Song. Hydrogen (H2) electrochemistry primarily consists of two reactions: hydrogen evolution reaction in water for H2 production (HER) and hydrogen oxidation reaction in hydrogen fuel cells for H2 utilization (HOR). The realiz

T. Leo Liu, Steve Scheiner, Jared B. Moss, Liping Zhang, Kevin V. Nielson, Yujing Bi. DFT calculations were conducted to provide unprecedented thermodynamic insights on tetrahydrofuran (THF) solvation, isomerization, and complexation of possible Mg􀀀 Cl

Nicholas E. Dickenson, Sean J. Johnson, Hannah J. Demler, Heather B. Case, Yalemi Morales, Abram R. Bernard. Like many Gram-negative pathogens, Shigella rely on a type three secretion system (T3SS) for injection of effector proteins directly into euka

Alexander I. Boldyrev. Because of their interesting structures and bonding and potentials as motifs for new nanomaterials, size-selected boron clusters have received tremendous interest in recent years. In particular, boron cluster anions (Bn−) have

Alexander I. Boldyrev, Nikolay V. Tkachenko, Ivan A. Popov, Nikita Fedik.

Steve Scheiner. Four H-binding HCl and HF molecules position themselves at the vertices of a tetrahedron when surrounding a central Cl−. Halogen bonding BrF and ClF form a slightly distorted tetrahedron, a tendency that is amplified for ClCN which fo

Steve Scheiner. One of several tetrel (T) atoms was covalently attached to three F atoms and a substituted phenyl ring. A NH3 base can form a tetrel bond with TF3C6H2R3 (T = Si, Ge, Sn, Pb; R = H, F, CH3) in a position opposite either an F atom or the r

Alexander I. Boldyrev, Maksim Kulichenko. Abstract: In a high-resolution photoelectron imaging and theoretical study of the IrB3 @ cluster, two isomers were observed experimentally with electron affinities (EAs) of 1.3147(8) and 1.937(4) eV. Quantum cal

Steve Scheiner. (MY)6 clusters, with M = Zn and Cd and Y = O, S, Se, form double-layer drum-like structures containing M–Y covalent bonds. The positive regions near the M atoms attract the N atom of both NH3 and NMe3 so as to form a noncovalent M···N b

Alexander I. Boldyrev, Nikolay Tkachenko. A novel approach to chemical bond analysis for excited states has been developed. Using an extended adaptive natural density partitioning method (AdNDP) as implemented in AdNDP 2.0 code, we obtained chemicall

Lance C. Seefeldt, T. Leo Liu, Maowei Hu, Bo Hu. Instead of catalyzing electrochemical reduction of N2, we found that tetragonal Mo2N undergoes decomposition and results in the generation of ammonia. The present results call urgent attention to the need

Lisa M. Berreau, Tatiana Soboleva Carbon monoxide-releasing molecules (CORMs) that enable the delivery of controlled amounts of CO are of strong current interest for applications in biological systems. In this review, we examine the various conditio

Tianbiao Leo Liu, Jian Luo, Yujing Bi, Liping Zhang, Xiaoyin Zhang. Mg batteries are a promising energy storage system because of the physicochemical merits of Mg as an anode material. However, the lack of electrochemically and chemically stable Mg e

Alexander I. Boldyrev, Maksim Kulichenko, Nikita Fedik. Growing demands of material science and, in particular, in the field of nonlinear optics (NLO) encourage us to look for stable highly polarizable molecules with excess diffuse electrons. An unusua

T. Leo Liu, Jian Luo, Wenda Wu, Camden Debruler, Bo Hu, Maowei Hu. Aqueous redox flow batteries using low-cost organic and inorganic active materials have received growing interest for sustainable energy storage. In this study, a low-cost, high redox po

Lance C. Seefeldt, Zhi-Yong Yang. The Mo-dependent nitrogenase comprises two interacting components called the Fe protein and the MoFe protein. The MoFe protein is an a2b2 heterotetramer that harbors two types of complex metalloclusters, both of which a

Alvan C. Hengge Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes know...

Alexander I. Boldyrev, Nikita Fedik, Maksim Kulichenko. Amidst the general bonding patterns designed to explain stability aromaticity has leading role. Going far away beyond classic notion of organic chemistry aromaticity was proven to be a useful to

Steve Scheiner. In order to accommodate the approach of two NCH bases, a tetrahedral TF4 molecule (T=Si, Ge, Sn, Pb) distorts into an octahedral structure in which the two bases can be situated either cis or trans to one another. The square planar geom

Lisa M. Berreau, Tatiana Soboleva Carbon monoxide (CO) is a bioactive signalling molecule that is produced endogenously via the breakdown of heme. Beneficial health effects associated with the delivery of CO gas have spurred the development of CO‐relea

Yi Rao. Adsorption of the carboxylic anchoring dye, pethyl red (p-ER), onto TiO2 nanoparticles in protic vs aprotic solvents was studied in situ using the surface-specific technique, second harmonic light scattering (SHS). Two different adsorption sch

Steve Scheiner. The complexes between borazine and TH3F/F2TO/H2TO (T = C, Si, Ge) are investigated with high‐level quantum chemical calculations. Borazine has three sites of negative electrostatic potential: the N atom, the ring center, and the H atom

Cheng-Wei Tom Chang, Yagya Prasad Subedi Amphiphilic aminoglycosides have attracted interest due to their novel antifungal activities. A crucial but often neglected factor for drug development in academia is cost of production. Herein is reported a one-st...

T. Leo Liu, Jian Luo, Bo Hu, Camden Debruler, Yujing Bi, Maowei Hu, Wenda Wu. Aqueous organic/organometallic redox flow batteries (AORFBs) have gained increasing attention for large-scale storage of intermittent renewable energy (e.g., solar and wind) d

Alexander I. Boldyrev, Nikita S. Fedik. Using the DFT methods, we computationally predict the stability of cage compounds E4nRn (E = B, C; R = H, F; n = 4, 8, 12, 24) based on Platonic bodies and Archimedean polyhedrons in which all vertices are replace

Lance C. Seefeldt. The ammonium-dependent posttranslational regulation of nitrogenase activity in Azospirillum brasilense requires dinitrogenase reductase ADPribosyl transferase (DraT) and dinitrogenase reductase ADP-glycohydrolase (DraG). These enzymes

Lance C. Seefeldt, Zhi-Yong Yang. Pg. 231-251. Nitrogenases are complex two-component metalloenzymes that catalyze biological nitrogen fixation. Three different nitrogenase types are found in the model nitrogen-fixing microbe azotabacter vinelandii. In

Cheng-Wei Tom Chang, Yagya Prasad Subedi Development of new antibiotics is always needed in the fight against growing threat from multiple drug–resistant bacteria, such as resistant Gram-negative (G−) Escherichia coli and Klebsiella pneumoniae. While

Heather B. Case, Dominic S. Mattock and Nicholas E. Dickenson Many important human pathogens rely on one or more type three secretion systems (T3SSs) to inject bacterial effector proteins directly into the host cell cytoplasm. Secretion of protein through...

T. Leo Liu, Jian Luo. In this issue of Chem, Jin and coworkers present the design principles and demonstration of a highly efficient integrated solar flow battery (SFB) device that can be configured to perform all the requisite functions from solar ener

Steve Scheiner. The carbene triel bond is predicted and characterized by theoretical calculations. The C lone pair of N‐heterocyclic carbenes (NHCs) is allowed to interact with the central triel atom of TrR3 (Tr = B and Al; R = H, F, Cl, and Br). The en

Yagya Prasad Subedi, madher N. Alfindee, Jaya P. Shestha, and Cheng-Wei Tom Chang Abstract: Development of new antibacterial agents against drug resistant bacteria is an imminent task, especially against methicillin-resistant Staphylococcus aureus (MRSA)....

Yuqin Qian, Gang-hua Deng, and Yi Rao The gas–aerosol particle interface is believed to contribute to the growth of secondary organic aerosols in the atmosphere. Despite its importance, the chemical composition of the interface has not been probed directl...

Lance C. Seefeldt. Electron bifurcation, or the coupling of exergonic and endergonic oxidation-reduction reactions, was discovered by Peter Mitchell and provides an elegant mechanism to rationali

Tatiana Soboleva, Hector J. Esquer, Stacey N. Anderson, Lisa M. Berreau, and Abby D. Benninghoff ABSTRACT: While interactions between carbon monoxide (CO) and mitochondria have been previously studied, the methods used to deliver CO (gas or CO-releasing m...

Ivan A. Popov, Elisa Jimenez-Izal, Anatassia N. Alexandrova and Alexander I. Boldyrev ABSTRACT: We have studied the electronic structure of F-centers in the bulk and on the (100) surface of the MgO crystal. Chemical bonding analysis was performed using t...

Yagya Prasad Subedi, Madher N. Alfinee, Jon Y. Takemoto and Cheng-Wei Tom Chang Classical aminoglycoside antibiotics are obsolete or hampered by the emergence of drug resistant bacteria. Recent discoveries of antifungal amphiphilic kanamycins offer new

Heather B. Case and Nicholas E. Dickenson: Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at th...

Jared B. Moss, Upendra Adhikari, and Steve Scheiner: Thermodynamic quantities ΔEelec, ΔH, and ΔG are computed by various different levels of ab initio quantum theory. The values obtained are searched for any reversals in order of stability between differe...

Methyl viologen (MV) as a bench-mark anolyte material has been frequently applied in aqueous organic redox flow batteries (AORFBs) towards large-scale renewable energy storage. However, only the first reduction of MV was utilized in aqueous electrolytes b...

Madher N. AlFindee, Qian Zhang, Yagya Prasad Subedi, Jaya P. Shrestha, Yukie Kawasaki, Michelle Grilley, Jon Y. Takemoto, Cheng-Wei Tom Chang: Carbohydrate esters are biodegradable, and the degraded adducts are naturally occurring carbohydrates and fatty ...

Tamar B. Caceres, Abhishek Thakur, Owen M Price, Nicole Ippolito, Jun Li, Jun Qu, Orlando Acevedo and Joan Hevel ABSTRACT: Protein arginine methyltransferase 7 (PRMT7) is unique within the PRMT family as it is the only isoform known to exclusively make m...

Extending the conjugation of viologen by a planar thiazolo[5,4-d]thiazole (TTz) framework and functionalizing the pyridinium with hydrophilic ammonium groups yielded a highly water-soluble π-conjugation extended viologen, 4,4′-(thiazolo[5,4-d]thiazole-2,5...

Tatiana Soboleva, Abby D. Benninghoff, and Lisa M. Berreau: Signaling molecules, including H2S and CO, are involved in a complex interplay within cells to maintain cellular homeostasis. In order to investigate the intracellular interplay of different gaso...

Miguel Martinez-Canales, Timur R. Galeev, Alexander I. Boldyrev, and Chris J. Pickard: We introduce two-dimensional borane, a single-layered material of BH stoichiometry, with promising electronic properties. We show that, according to Density Functional ...

Paul B. G. van Erp, Angela Patterson, Ravi Kant, Luke Berry, Sarah M. Golden, Brittney L. Forsman, Joshua Carter, Ryan N. Jackson, Brian Bothner, and Blake Wiedenheft: Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic ...

Shayne Sorenson, Marina Popova, Atta M. Arifb and Lisa M. Berreau: Metal–flavonolate compounds are of significant current inter­est as synthetic models for quercetinase enzymes and as bioactive compounds of importance to human health. Zinc–3-hy­droxy­fla...

Yuan Chu, Nicholas H. Williams, and Alvan C. Hengge : Catalytically promiscuous enzymes are an attractive frontier for biochemistry, because enzyme promiscuities not only plausibly explain enzyme evolution through the mechanism of ge...

Jackson, R., van Erp, P.B, Sternberg, S.H, Wiedenheft, B.: Adaptive immune systems in bacteria and archaea rely on small CRISPR-derived RNAs (crRNAs) to guide specialized nucleases to foreign nucleic acids. The activation of these nucleases is controlled ...

Aebig, C.H.F., Curtin, L., Hageman, K.J., Moy, C.M., Beltran, C.: Organic biomarkers, such as n-alkanes, can be used as proxies in a range of paleoclimate and paleoenvironmental investigations. n-Alkanes accumulate in lacustrine sediments and can therefor...

D.D. Markushev, J. Ordonez-Miranda, M.D. Rabasovi´c, M. Chirtoc, D.M. Todorovi´c, S.E. Bialkowski, D. Korte, and M. Franko: A portable photoacoustic device is designed and applied to measure thermal diffusivity and linear thermal expansion coefficient of ...