Bruce F Milne

Bruce F Milne
University of Coimbra | UC · Department of Physics

PhD Chemistry

About

83
Publications
8,495
Reads
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1,268
Citations
Citations since 2016
24 Research Items
650 Citations
2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
Introduction
Bruce F Milne currently works at CFisUC, Department of Physics, University of Coimbra. Bruce does research in Atomic, Molecular and Optical Physics, Computational Physics and Physical Chemistry.
Additional affiliations
September 2018 - present
University of Coimbra
Position
  • Researcher
September 2017 - August 2018
University of Coimbra
Position
  • Researcher
October 2013 - present
Universidad del País Vasco / Euskal Herriko Unibertsitatea
Position
  • Researcher

Publications

Publications (83)
Article
Full-text available
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex natural products with diverse bioactivities. Here we report discovery of a RiPP, kintamdin, for which the structure is determined through spectroscopy, spectrometry and genomic analysis to feature a bis -thioether macrocyclic ring and a β-enamino aci...
Article
Vibrational and electronic absorption spectra calculated at the (time-dependent) density functional theory level for the bismuth carbide clusters BinC2n+ (3⩽n⩽9) indicate significant differences in types of bonding that depend on cluster geometry. Analysis of the electronic charge densities of these clusters highlighted bonding trends in these comp...
Preprint
Full-text available
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex naturally occurring metabolites across all three domains of life. Despite the structural diversity of RiPPs that stems from the extensive post-translational modifications, only α-amino acid residues have been found in known RiPPs. Here we report disc...
Preprint
Full-text available
Vibrational and electronic absorption spectra calculated at the (time-dependent) density functional theory level for the bismuth carbide clusters Bi$_{n}$C$_{2n}$$^+$ ($3 \le n \le 9$) indicate significant differences in types of bonding that depend on cluster geometry. Analysis of the electronic charge densities of these clusters highlighted bondi...
Preprint
Full-text available
Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. Our approach uniquely combines crowdsourced medicinal chemistry insights with high throughput crystallography, exascale computational chemistry infrastructure for simulations, and machi...
Article
Full-text available
Platinum metal complexes are the most common chemotherapeutics currently used in cancer treatment. However, the frequent adverse effects, as well as acquired resistance by tumor cells, urge the development of effective alternatives. In the recent past, copper complexes with Schiff base ligands have emerged as good alternatives, showing interesting...
Article
Full-text available
As opposed to small molecules, macrocyclic peptides possess a large surface area and are recognised as promising candidates to selectively treat diseases by disrupting specific protein-protein interactions (PPIs). Due to the difficulty in predicting cyclopeptide conformations in solution, the de novo design of bioactive cyclopeptides remains signif...
Article
Full-text available
The physics of surface plasmons has a long tradition in condensed matter theory but as the dimension of the systems reaches the nano scale, new effects appear. In this work, by calculating the absorption spectra of a single wall carbon nanotube, using time dependent density functional theory, the effect of adding/removing electrons on the surface p...
Article
Full-text available
In certain materials, and for certain voltage ranges, electrical current flowing through the material decreases when the voltage across the sample is increased. This negative differential conductance (NDC) is important for oscillators, amplifiers, and fast switching devices. In this work, using real-time quantum simulations, we show that this pheno...
Article
A necessary first step in the development of technologies such as artificial photosynthesis is understanding the photoexcitation process within the basic building blocks of naturally occurring light harvesting complexes (LHCs). The most important of these building blocks in biological LHCs such as LHC II from green plants are the chlorophyll a (Chl...
Preprint
Full-text available
A necessary first step in the development of technologies such as artificial photosynthesis is understanding the photoexcitation process within the basic building blocks of naturally-occurring light harvesting complexes (LHCs). The most important of these building blocks in biological LHCs such as LHC II from green plants are the chlorophyll $a$ (C...
Article
In order to accelerate the isolation and characterization of structurally new or novel secondary metabolites, it is crucial to develop efficient strategies that prioritize samples with greatest promise early in the workflow so that resources can be utilized in a more efficient and cost-effective manner. We have developed a metrics-based prioritizat...
Article
A library of new chiral thiazolidines was prepared starting from L-cysteine and D-penicillamine in a simple, one-step procedure. 2-Arylthiazolidines were obtained, as diastereoisomeric mixtures, with good yields and in short reaction times, through a new and greener procedure, using microwave irradiation. Their use as chiral ligands in the enantios...
Article
Cyclodextrins (Cds) are versatile carbohydrate hosts for developing multifunctional nanostructures of pharmaceutical interest. Factors affecting the thermodynamic signatures and stability of β- and γ-Cd complexes are detailed at the atomic level. The MD/PMF-based method is combined with the description of the nature and strength of the inter-partne...
Preprint
Full-text available
First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate th...
Article
First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate th...
Article
The critical roles of solvent, enthalpic, and entropic contributions in complexes between different hyaluronic acid derivatives bearing monomeric β-cyclodextrin and adamantene moieties are assessed combining our previously designed free energy oriented method and a recently proposed density-based noncovalent interaction analysis. This establishes t...
Article
Full-text available
The crystal structures of ( E )-1-methyl-5-nitro-1 H -imidazole-2-carbaldehyde O -benzyloxime, C 12 H 12 N 4 O 3 , (I), ( E )-1-methyl-5-nitro-1 H -imidazole-2-carbaldehyde O -(4-fluorobenzyl) oxime, C 12 H 11 FN 4 O 3 , (II), and ( E )-1-methyl-5-nitro-1 H -imidazole-2-carbaldehyde O -(4-bromobenzyl) oxime, C 12 H 11 BrN 4 O 3 , (III), are describ...
Article
Full-text available
Exciton coupling between two or more chlorophyll (Chl) pigments is a key mechanism associated with the color tuning of photosynthetic proteins but it is difficult to disentangle this effect from shifts that are due to the protein microenvironment. Herein, we report the formation of the simplest coupled system, the Chl a dimer, tagged with a quatern...
Article
Full-text available
Action spectroscopy provides key insights into the nature of electronic transitions of coordination complexes such as porhyrin-containing biochromophores like chlorophyll or transition metal complexes such as tris(bipyridine)ruthenium.
Article
Full-text available
First-principles calculations within the framework of real-space time-dependent density functional theory have been performed for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible studies of the optical response of individual Chl...
Article
Full-text available
We have performed gas-phase absorption spectroscopy in the Soret-band region of chlorophyll (Chl) a and b tagged by quaternary ammonium ions together with time-dependent density functional theory (TD-DFT) calculations. This band is the strongest in the visible region of metalloporphyrins and an important reporter on the microenvironment. The cation...
Article
Full-text available
A novel erbium(III) complex with acetylacetone (Hacac) and bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, bath) ligands, formulated as [Er(acac)3(bath)], has been characterized by elemental analysis, X-ray diffraction, thermogravimetric analysis, Fourier transform infrared spectroscopy, Raman spectroscopy, absorption and emission spectrosco...
Article
The first-order hyperpolarizability, β, has been calculated for a group of marine natural products, the makaluvamines. These compounds possess a common cationic pyrroloiminoquinone structure that is substituted to varying degrees. Calculations at the MP2 level indicate that makaluvamines possessing phenolic side chains conjugated with the pyrroloim...
Article
The exact color of light absorbed by chlorophyll (Chl) pigments, the light-harvesters in photosynthesis, is tuned by the protein microenvironment, but without knowledge of the intrinsic color of Chl it remains unclear how large this effect is. Experimental first absorption energies of Chl a and b isolated in vacuo and tagged with quaternary ammoniu...
Article
Full-text available
The exact color of light absorbed by chlorophyll (Chl) pigments, the light-harvesters in photosynthesis, is tuned by the protein microenvironment, but without knowledge of the intrinsic color of Chl it remains unclear how large this effect is. Experimental first absorption energies of Chl a and b isolated in vacuo and tagged with quaternary ammoniu...
Article
Crystallography reveals the rotomer in the salt isolated from EtOH solution has an anti disposition of the OH and imine-NH hydrogen atoms while that from EtOCH2CH2OH solution has a syn disposition. Both molecules have an E configuration about the C=N bond and are essentially planar (dihedral angles between aromatic groups = 2.4 (3)° and 6.42 (9)°,...
Article
Full-text available
Time-dependent density functional theory has been used to investigate the effects of group 15/16 element substitution on the optical response of firefly oxyluciferin. A range of analogues containing symmetrical substitutions at the N and S atom positions of the naturally-occurring oxyluciferin have been found to have red-shifted electronic excitati...
Article
Full-text available
The optical absorption spectra and quadratic hyperpolarisabilities of 1,3,5,7-tetra-substituted cubane derivatives containing group 15 atoms have been investigated computationally using Coulomb-attenuated time-dependent density functional theory. The non-linear optical responses of these octupolar systems are shown to be highly dependent on the gro...
Article
The oxyluciferin molecule in its anionic form is responsible for light emission from fireflies and some railroad worms and click beetles. Here we have studied the breakdown of the ions after photoexcitation by 550-nm light, and identified the atom composition of eight fragment ions based on mass spectrometric experiments on isotope-labeled compound...
Article
Full-text available
Theoretical analysis using quadratic response theory within the time-dependent density functional theory (TDDFT) formalism shows that the dermacozines, a group of phenazine-based compounds isolated from cultures of Dermacoccus abyssi found in the Mariana Trench, possess large first hyperpolarisability (β) values at common incident laser wavelengths...
Article
A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive since it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here we use action spectroscopy to c...
Article
Full-text available
Nitrogen is a common structural element in the acceptor moieties of organic donor-acceptor nonlinear optical (NLO) chromophores. In order to assess the effect of substitution with heavier group 15 elements, computational studies of the nonlinear optical properties of betaine derivatives, (CH(3))(3)X(+)CH(2)CO(2)(-) (X = N, P, As, Sb, Bi), have been...
Poster
Full-text available
Heavy atom NLO enhancement in group 15 organometallics
Poster
Full-text available
Marine natural products: a new source of novel chromophores for nonlinear optics
Conference Paper
The special interest in molecular design for the development of novel second-order nonlinear optical (SONLO) materials is driven by their potential applications in new optoelectronic technologies. Various strategies are currently employed to enhance the molecular SONLO activity, and studies revealed that species having open-shell electronic states...
Article
The excited-state physics of the firefly luciferin anion depends on its chemical environment, and it is therefore important to establish the intrinsic behavior of the bare ion. Here we report electronic absorption spectra of the anion isolated in vacuo obtained at an electrostatic ion storage ring and an accelerator mass spectrometer where ionic di...
Poster
Full-text available
Gas phase spectroscopy of the firefly luciferin anion: comparison of experiment with TDDFT predictions
Article
In the current manuscript we present the results of a computational study on a series of chromophores with enhanced intrinsic hyperpolarizability. The high hyperpolarizability values of these molecules were previously reported and were achieved by making use of aromatic moieties in order to modulate the aromatic stabilization energy along the conju...
Article
Full-text available
Firefly bioluminescence displays a sensitivity to pH changes through an alteration of the energy of the emitted photon leading to yellow-green light above ∼pH 6.5 and red light below this value. Calculations using the fragment molecular orbital method have been performed on the active site of the luciferase enzyme from the Japanese firefly Luciola...
Article
We propose the heterojunction effect in the analysis of the fluorescence mechanism of the firefly chromophore. Following this analysis, and with respect to the HOMO-LUMO gap alignment between the chromophore's functional fragments, three main heterojunction types (I, II, and I*) are identified. Time-dependent density-functional theory optical absor...
Article
Bioassay-guided fractionation of the sub-Arctic ascidian Synoicum pulmonaria collected off the Norwegian coast led to the isolation of a novel family of brominated guanidinium oxazolidinones named synoxazolidinones A and B (1 and 2). The backbone of the compounds contains a 4-oxazolidinone ring rarely seen in natural products. The structure of the...
Article
Full-text available
Dermacoccus abyssi sp. nov., strains MT1.1 and MT1.2 are actinomycetes isolated from Mariana Trench sediment at a depth of 10 898 m. Fermentation using ISP2 and 410 media, respectively, lead to production of seven new oxidized and reduced phenazine-type pigments, dermacozines A-G (1-7), together with the known phenazine-1-carboxylic acid (8) and ph...
Poster
Full-text available
Spectroscopic and TD-DFT studies of solvent effects on the firefly luciferin anion. 2. Binary water:methanol solvents
Poster
Full-text available
Spectroscopic and TD-DFT studies of solvent effects on the firefly luciferin anion. 1. Gas and aqueous phases
Article
The MeO2CCH2CH2 ligand in X3SnCH2CH2CO2Me, (X = Cl, Br or I), acts as a C,O-chelating group, via the carbonyl group, both in the solid state and in solutions in non-coordinating solvents. The crystal structures of 1 (X = Cl), a redetermination at 120 K and of I (X = Br), at 298 and 120 K, are reported. Comparison of the intramolecular SnO bond leng...
Poster
Bio-heteroJunction effect on fluorescence origin and efficiency improvement of firefly chromophores
Poster
Fragment molecular orbital studies of luciferase from the Japanese firefly Luciola cruciata
Poster
Fragment molecular orbital studies of luciferase from the Japanese firefly Luciola cruciata
Poster
Time-dependent DFT for elucidation of stereochemistry: dermacozine E, a natural product from the Mariana Trench
Poster
Fragment molecular orbital studies of luciferase from the Japanese firefly Luciola cruciata
Article
Sequestering sea squirts: Liquid chromatography with parallel inductively coupled plasma mass spectrometry/electrospray mass spectrometry was used to discover and identify novel lipophilic metal complexes in the solvent extract of the ascidian Eudistoma gilboviride. Using these tools it is now possible to examine whether such complexes play an inte...
Article
In this work we present results of density functional theory (DFT) calculations on dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cycl...
Article
Dermacoccus abyssi sp. nov., MT1.1, is a piezotolerant actinobacterial strain isolated from Mariana Trench sediment at a depth 10898m. The fermentation process using ISP2 medium lead to production of several new and novel pigmented heteroaromatic (oxidised and reduced) phenazine compounds. Extensive use was made of 1D, 2D NMR data and high resoluti...
Article
Full-text available
Mercury in plants or animal tissue is supposed to occur in the form of complexes formed with biologically relevant thiols (biothiols), rather than as free cation. We describe a technique for the separation and molecular identification of mercury and methylmercury complexes derived from their reactions with cysteine (Cys) and glutathione (GS): Hg(Cy...