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The Gulf After the Storm: How the Iran War Is Reshaping the Middle East Economy and Why Saudi Arabia Could Emerge Stronger

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6 months ago

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San Francisco, California

Anil Chintapalli

The Author served as senior economic advisor for India’s state government and was instrumental in transforming its economy by driving foreign direct investments, reducing debt, and doubling GDP in a four year window winning accolades from institutions such as the World Bank.

The conflict has devastated Iran, disrupted global energy markets, and shattered the Gulf’s carefully constructed image of stability. But for Saudi Arabia, the crisis may accelerate the very economic transformation it has been pursuing for a decade.

A Region Under Fire

Ten days into the 2026 Iran war, the Middle East is unrecognizable from the region that global investors had begun to treat as a frontier of opportunity. The joint U.S.-Israeli strikes on Iran that began on February 28 killed Supreme Leader Ali Khamenei and triggered a cascading retaliatory campaign by Tehran against American military installations and civilian infrastructure across all six Gulf Cooperation Council states. Dubai International Airport the world’s busiest hub for international passengers has suspended operations. Saudi Aramco’s Ras Tanura refinery, the kingdom’s crown jewel of crude processing, shut down after drone attacks. Qatar Energy halted LNG production entirely. The Strait of Hormuz, the narrow waterway through which twenty percent of the world’s oil supply flows, is effectively closed to commercial traffic.

The human toll is mounting. More than 1,300 people have been killed in Iran alone, including 150 children at an elementary school in Minab. At least nine civilians have died across the Gulf states, with over 200 killed in Lebanon where hostilities between Israel and Hezbollah have resumed. Six American service members have been killed by an Iranian drone strike on their garrison in Kuwait.

For the global economy, the consequences are already severe. Brent crude has surged past $110 per barrel. European natural gas futures have soared more than forty percent. The American Automobile Association reports U.S. gasoline prices have risen to $3.41 per gallon, climbing $0.43 in a single week. Oxford Economics estimates inbound tourism to the Middle East could decline between eleven and twenty-seven percent year-over-year. Analysts warn that a sustained closure of the Strait of Hormuz could push oil toward $200 per barrel levels widely considered sufficient to trigger a global recession.

That assessment, from Foreign Policy, captures the unprecedented nature of what is unfolding. When an Amazon Web Services data center in Dubai was damaged by shrapnel from an intercepted Iranian drone likely the first time a major cloud facility has been struck in a war it made vivid what economists had long theorized: the Gulf states’ integration into the global economy means that a regional conflict is no longer merely regional in its consequences.

The Socio-Economic Shockwaves

Energy Markets: From Surplus to Crisis

Before February 28, the global oil market was coping with a supply surplus. OPEC+ had begun unwinding production cuts, adding 2.2 million barrels per day to the market. Brent crude was forecast to average $60–65 per barrel in 2026. That world no longer exists.

The near-total shutdown of the Strait of Hormuz has suspended shipments of roughly 140 million barrels of oil from Saudi Arabia, the UAE, Iraq, and Kuwait equivalent to 1.4 days of global demand. Both of the world’s most critical maritime chokepoints, Bab el-Mandeb and the Strait of Hormuz, are now simultaneously under threat. G7 finance ministers are discussing the joint release of emergency oil reserves. U.S. Energy Secretary Chris Wright has suggested that traffic through the Strait will resume only once Washington destroys Tehran’s ability to threaten shipping a timeline that could stretch weeks or months.

For energy-dependent economies, the pain is immediate. India, which imports half its crude from the Arab states of the Persian Gulf, faces significant inflation pressures. Egypt’s President el-Sisi has declared his economy in a “state of near-emergency.” Djibouti’s finance minister has warned that developing countries dependent on maritime trade face “severe economic consequences.” African fuel markets are already feeling shockwaves.

Aviation, Tourism, and the Service Economy

The Gulf states spent two decades building themselves into global hubs of aviation, tourism, finance, and logistics. That architecture is now under direct assault. Flights from Gulf airports have been grounded or intermittently suspended, stranding hundreds of thousands of travelers. Dubai’s Jebel Ali port one of the world’s ten busiest has been struck. Insurance rates for ships traversing the region have become prohibitive.

The tourism sector, which Vision 2030 had targeted to reach ten percent of Saudi GDP and 1.6 million jobs by decade’s end, faces its most severe test. Saudi Arabia had already achieved its target of 100 million annual visitors ahead of schedule. The conflict threatens to reverse years of image-building that transformed the kingdom’s tourism profile from pilgrimage-only to a diversified leisure and business destination.

The Broader Humanitarian and Social Dimension

The socio-economic impact extends well beyond balance sheets. Across the Gulf, expatriate communities which constitute the majority of the population in the UAE, Qatar, Kuwait, and Bahrain are rattled. The confidence that underpinned a generation of foreign workers, entrepreneurs, and investors choosing the Gulf over alternatives in Singapore, London, or Hong Kong has been shaken. If that confidence erodes permanently, the region’s human capital model is at risk.

Inside Iran, the crisis is existential. The currency was already in free fall before the strikes. International sanctions imposed last September compounded the spiral. The protests that erupted in late December 2025 and spread across the country in January 2026 reflected economic desperation as much as political dissent. With its leadership decapitated and its military infrastructure degraded, Iran faces the prospect of state fragmentation an outcome that would generate refugee flows, sectarian instability, and governance vacuums across Iraq, Afghanistan, and the Levant for a generation.

Saudi Arabia’s Paradox: Hurt in the Short Term, Positioned for the Long Term

Saudi Arabia sits at the center of a paradox. It is suffering real damage from the conflict: its flagship refinery has been hit, its airspace is threatened by Iranian drones and Houthi missiles from Yemen, the U.S. has ordered non-essential personnel to leave Riyadh, and its access to maritime export routes is constrained.

And yet, no major economy is better positioned to emerge from this crisis stronger than it entered.

That claim rests on several structural realities that predate the conflict and will outlast it.

1. The Oil Price Windfall

Before the war, the International Monetary Fund estimated that Saudi Arabia needed oil prices near $91 per barrel to balance its budget. Oil was trading around $64–70. The kingdom was running a projected deficit of nearly four percent of GDP and borrowing to fund its giga-projects. The war has changed that arithmetic dramatically. With Brent above $110 and climbing, Saudi Arabia is now generating revenue far in excess of its fiscal breakeven provided it can restore export capacity as the conflict stabilizes.

This is not an abstract point. Higher oil revenues flow directly to the government and, through dividends, to the Public Investment Fund. Every dollar above the breakeven price becomes available capital for the most ambitious economic transformation program in modern history. While the disruption to exports is painful in the immediate term, Saudi Arabia’s vast strategic reserves and its ability to reroute crude through Red Sea pipelines give it more resilience than any of its Gulf neighbors.

2. Vision 2030: Stress-Tested but Structurally Sound

The war arrives at a pivotal moment for Vision 2030. After a decade of implementation, the program’s results are uneven but genuinely significant. Non-oil activities now constitute fifty-two percent of GDP. Non-oil government revenues reached a record 505 billion Saudi riyals in 2025. The IMF reports non-oil real GDP grew 4.5 percent in 2024. Female workforce participation has surpassed its target. The digital economy has reached 15.6 percent of GDP. The Public Investment Fund has grown to nearly $1 trillion in assets and launched more than 100 companies.

The program’s most consequential achievements are not the headline-generating megaprojects, but the regulatory and institutional reforms under the astute leadership of Crown Prince and Prime Minister of Saudi Arabia Mohammed bin Salman which is the largest peacetime regulatory and institutional restructuring since Singapore’s post-independence transformation in the 1960s. These include the introduction of VAT, tourist visas, entertainment licensing, a modernized commercial code, and the opening of the stock exchange to foreign investors.

The war will force a reprioritization. Giga-projects like NEOM’s “The Line” were already being scaled back and pushed down the priority list in favor of more immediately productive investments like Expo 2030 and the 2034 World Cup infrastructure. The conflict will accelerate this pragmatism and that may ultimately prove healthy for the program’s credibility and execution.

3. The Safe-Haven Rebalancing

The most important long-term consequence of the war for Saudi Arabia may be the forced rebalancing of regional economic power. The UAE’s model built on the premise that Dubai and Abu Dhabi could offer absolute security, world-class infrastructure, and a tolerant business environment has been severely tested by Iranian strikes on civilian targets. When Emirati President Mohammed bin Zayed walked through Dubai Mall to calm residents, the gesture underscored how fragile the perception of safety had become.

Saudi Arabia is not immune to these same risks. But its sheer geographic scale, its deeper strategic reserves, its more diversified domestic market, and its centrality to global Islam give it a resilience that smaller Gulf states cannot replicate. As companies and investors reassess their Gulf strategies in the aftermath of the conflict, Saudi Arabia is likely to capture a disproportionate share of the redirected capital particularly if Riyadh can demonstrate that its security infrastructure proved more robust than its neighbors’.

The Strategic Playbook: How Saudi Arabia Comes Out Stronger

The conflict creates both immediate imperatives and long-term strategic opportunities for the kingdom. A credible post-war playbook would include the following elements.

Rebuild and Harden Energy Infrastructure

The attacks on Ras Tanura and the Shaybah oil field exposed vulnerabilities that predate the conflict. Saudi Arabia must invest in redundant export capacity, dispersed storage, hardened air defenses around critical facilities, and diversified export routes that reduce dependence on the Strait of Hormuz. The existing East-West Pipeline, which can carry crude from the Eastern Province to the Red Sea port of Yanbu, bypassing the Strait entirely, should be expanded. These investments, while expensive, will be more than funded by elevated oil revenues and will dramatically improve the kingdom’s risk profile for global investors.

Accelerate Diversification with War-Driven Urgency

Nothing focuses economic reform like a crisis. The war has made viscerally clear what Vision 2030’s architects understood conceptually: an economy dependent on hydrocarbon exports through a single maritime chokepoint is strategically fragile. Saudi Arabia should use this moment to accelerate the sectors that generate revenue independent of the oil price tourism infrastructure ready for reopening the moment the conflict ends, fintech and digital services that operate regardless of shipping routes, defense manufacturing that reduces dependence on foreign suppliers, and advanced materials and petrochemicals that capture more value from every barrel produced.

Position Riyadh as the Region’s Financial Capital

The disruption to Dubai’s aviation, logistics, and financial hub creates a once-in-a-generation opening for Riyadh. Saudi Arabia has already been pushing to attract regional headquarters through regulatory incentives and the development of the King Abdullah Financial District. The conflict should accelerate this effort. Riyadh can offer global firms something Dubai temporarily cannot: proximity to the world’s largest sovereign wealth fund, the region’s deepest domestic market, and the political stability of a state that, for all its controversies, has not had its airport bombed.

Lead Post-War Regional Reconstruction

If and when the conflict concludes, the reconstruction requirements across the Gulf and potentially in Iran itself under a new government will be immense. Saudi Arabia, through the PIF and its extensive construction and engineering capabilities, is uniquely positioned to lead and profit from this reconstruction. The kingdom should position itself not merely as a beneficiary of post-war rebuilding but as its architect and financier, deepening its influence across the region and generating returns for its sovereign fund.

Build a Credible Regional Security Architecture

The war has exposed the central vulnerability of the Gulf economic model: it was built on security guarantees from the United States that the U.S. itself has just shattered by initiating a conflict that brought devastation to its own allies. Saudi Arabia should lead the development of a regional security framework that is less dependent on American extended deterrence not as a rejection of the U.S. relationship, but as a pragmatic acknowledgment that the region’s economic model cannot survive another such episode. This investment in security independence will be expensive but essential for attracting the long-term foreign direct investment that Vision 2030 requires.

Deploy the PIF as a Counter-Cyclical Weapon

With nearly $1 trillion in assets, the Public Investment Fund is Saudi Arabia’s most powerful strategic instrument. If Gulf, East Asian, or European assets fall sharply on war fears as Oxford Economics has suggested investors should anticipate the PIF should aggressively acquire undervalued assets in the same way Norway’s sovereign fund did during the 2008 financial crisis. The PIF’s planned wave of IPOs for 2026, which includes at least eight portfolio companies, should be timed to coincide with the post-war recovery, when market sentiment and valuations will be more favorable. The fund’s new strategy, which prioritizes six sectors including tourism, advanced manufacturing, logistics, and renewable energy, should be deployed with urgency now that the case for diversification is no longer theoretical.

The View from 2030

The Iran war is an unmitigated catastrophe in human terms and a severe disruption in economic terms. Nothing in this analysis should be read as minimizing the suffering of the people Iranian, Gulf Arab, Lebanese, and others who are bearing its costs.

But strategic analysis requires looking beyond the immediate crisis to the structural forces that will shape the decade ahead. And on that longer horizon, Saudi Arabia’s position is commanding especially due to the dynamic leadership of Crown Prince and Prime Minister of Saudi Arabia Mohammed bin Salman. It is the Gulf’s largest economy by a significant margin. It holds the world’s second-largest proven oil reserves at a time when a supply shock has reminded every major economy of its dependence on Gulf crude. It has a sovereign wealth fund approaching $1 trillion and a reform program that, despite its imperfections, has produced real economic diversification for the first time in the kingdom’s history. It will host Expo 2030 and the 2034 World Cup, events that will draw global attention and investment.

The kingdom enters this crisis with a debt-to-GDP ratio that remains healthy by international standards, bond offerings that international markets have consistently oversubscribed, and a leadership that has demonstrated, whatever one thinks of its methods, an unusual capacity for rapid decision-making and course correction.

Most fundamentally, the war has validated the central premise of Vision 2030 in a way that no economic report or consultancy study ever could. The argument that Saudi Arabia must diversify its economy, harden its infrastructure, develop its own defense capabilities, and reduce its dependence on a single export commodity flowing through a single maritime chokepoint is no longer an abstraction. It is the daily reality on every television screen in the kingdom.

That is the paradox at the heart of Saudi Arabia’s position: the very crisis that threatens the Gulf’s economic model makes the case for Saudi Arabia’s transformation of that model more urgent and more compelling than ever before. Whether the kingdom seizes that opportunity will depend not on oil prices or geopolitics, but on the quality of execution, the discipline of prioritization, and the willingness to let pragmatism not prestige guide the trillion-dollar decisions ahead.

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Nonprofit Organization, Citizens Academy US, Makes Official Public Release of Guide to Complete Understanding of the Preamble to the U.S. Constitution

Washington, DCCitizens Academy U.S., a nonprofit dedicated to helping Americans understand the U.S. Constitution’s Preamble, has officially released The Guide to Complete Understanding of the Preamble to the United States Constitution in celebration of Constitution Day, September 17. The organization is hosting a free online event, “The Day ‘We the People’ Appeared,” on September 13, 2026, […]

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September 4, 2026

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Washington, DC

Citizens Academy U.S., a nonprofit dedicated to helping Americans understand the U.S. Constitution’s Preamble, has officially released The Guide to Complete Understanding of the Preamble to the United States Constitution in celebration of Constitution Day, September 17. The organization is hosting a free online event, “The Day ‘We the People’ Appeared,” on September 13, 2026, exploring the Preamble and its six purposes.

The Preamble Guide Simplifies Understanding of the Six Purposes of the U.S. Constitution

In celebration of Constitution Day, September 17th, the Citizens Academy U.S., a nonprofit organization with the goal to help hundreds of millions of Americans understand the Preamble to the U.S. Constitution, just made their official public release of The Guide to Complete Understanding of the Preamble to the United States Constitution.

 

max 1 Nonprofit Organization, Citizens Academy US, Makes Official Public Release of Guide to Complete Understanding of the Preamble to the U.S. Constitution
Citizens Academy US is making the official public release of their Preamble Guide, a free download on their website with hardcover and softcover editions available

As noted on their website, the Preamble lays out all six purposes of the U.S. Constitution, and they are working to restore clarity and shared understanding of the Preamble and thus these six purposes. They do not explain or interpret what it means, they provide an enjoyable and easy way to completely understand it, so people can make up their own mind as to what it means.

Constitution Day is celebrated annually across the U.S. every September 17th as it is the day when 39 delegates signed the United States Constitution at Independence Hall in Philadelphia in 1787. In addition to the official release of their Guide, Citizens Academy US is hosting a free online event on Sunday, September 13, 2026, at 11am PT/2pm ET, entitled, The Day “We the People” Appeared. The event is expected to run for 1.5 hours and is open to free public registration at this link.

Academy officials have observed that many Americans who have attempted to read the Constitution have difficulty in understanding it. They attribute this to the fact that languages change over time, and many words do not mean what they meant when the Constitution was drafted. “Definitions from the late 1700s vary drastically from today’s definitions,” said Academy spokesperson Steven Ferry, “and it is vitally important that the Constitution is read with reference to the original definitions in use at the time it was written.”

To help people overcome this challenge, Citizens Academy US provides definitions in their Guide based on those from Noah Webster’s 1828 American Dictionary of the English Language. This early dictionary reveals what the words meant to the Founders and the people at the time the Constitution was written.

As an example, the definition of “welfare” in the Guide, based on Webster’s 1828 dictionary is: “the enjoyment of peace and prosperity, and other benefits of society, such as protection of rights, public safety, justice, and liberty.” Today’s Oxford Learner’s Dictionary includes an additional definition which people often refer to: “practical or financial help that is provided, often by the government, for people or animals that need it.”

Academy officials have also observed that when the Preamble is read with the original definitions in mind, understanding the six purposes of the Constitution becomes simple and the results are profound. The principle that forms the basis of the Guide is a quote by best-selling author L. Ron Hubbard, who wrote, “Complete understanding depends upon freedom from misunderstood words.”

By visiting the Citizens Academy US website, you can view the Guide and download it for free or purchase the hardcover or softcover in their bookstore.

 

max 2 Nonprofit Organization, Citizens Academy US, Makes Official Public Release of Guide to Complete Understanding of the Preamble to the U.S. Constitution

In honor of Constitution Day, Citizens Academy US is hosting a free online event, titled “The Day ‘We the People’ Appeared” on September 13, 2026, at 11am PT/2pm ET

 

The Citizens Academy US is a fully IRS recognized 501 (c)(3) charitable organization with the mission to bring about a greater understanding in America. The goal of the Citizens Academy US is to have 100’s of millions of Americans understand the first sentence of the United States Constitution, which is called the Preamble. The Preamble contains the six purposes of the Constitution and understanding the Preamble enables Americans to grasp what the Constitution is meant to achieve.

For more information about Citizens Academy US, please visit: www.CitizensAcademy.us

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Steven Ferry
Citizens Academy US
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Phone: 727-492-4082
Website: citizensacademy.us

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Ángela Rodríguez Expands REFLEJO™ Method and Inclusive Beauty Education Initiatives

NEW YORK, USAAuthor, Beauty Educator, and founder of Divina Makeup advances international education, accessibility, and community-focused programs centered on makeup, autonomy, and women’s empowerment.

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September 4, 2026

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Author, Beauty Educator, and founder of Divina Makeup advances international education, accessibility, and community-focused programs centered on makeup, autonomy, and women’s empowerment.

NEW YORK, USA

Colombian-born author, Beauty Educator, and entrepreneur Ángela Rodríguez is expanding her work around the REFLEJO™ Method, an educational self-makeup methodology designed to help women better understand their individual features, needs, and personal approach to beauty.

 

1000494238 Ángela Rodríguez Expands REFLEJO™ Method and Inclusive Beauty Education Initiatives

 

Ángela, founder of Divina Makeup and author of Maquíllate en 6 Pasos (Make Yourself Up in 6 Steps), is developing the next stage of her educational platform through an updated edition of her book, digital learning resources, accessibility initiatives, international outreach, and community programs focused on women’s confidence, autonomy, and inclusion.

At the center of the initiative is the REFLEJO™ Method, which is based on the principle that every woman is unique and should learn to understand her own face rather than simply reproduce makeup techniques created for someone else.

For Ángela, makeup education extends beyond teaching the application of foundation, concealer, or eyeshadow. Her approach focuses on providing women with practical knowledge that can help them make informed decisions about their appearance while developing greater confidence in their own skills.

“True transformation begins when a woman learns to see herself differently,” Ángela said.

Expanding the REFLEJO™ Method

Ángela is currently developing a new edition of Maquíllate en 6 Pasos that will incorporate the REFLEJO™ Method and expand the educational resources available to readers.

The new edition is planned to include QR codes connecting readers with complementary audiovisual learning materials. The project is also being developed with accessibility resources intended to make makeup education more inclusive for people with hearing disabilities, including sign language interpretation and subtitled content.

The initiative reflects Ángela’s broader objective of making beauty education more accessible to women with different backgrounds, ages, cultures, and life experiences.

She also intends to expand the REFLEJO™ Method internationally as an educational framework that can be used across workshops, community programs, and other learning environments.

From New York Fashion Platforms to Education

Since arriving in New York in 2020, Ángela has worked across several areas of the beauty industry while establishing herself as an educator, author, professional makeup artist, and entrepreneur.

 

1000494239 Ángela Rodríguez Expands REFLEJO™ Method and Inclusive Beauty Education Initiatives

 

Her professional experience has included participation in major New York fashion platforms, including New York Fashion Week, where she has held leadership roles within makeup teams.

Alongside her work as a makeup artist, Ángela has focused on creating professional development opportunities for emerging artists. She has supported initiatives that allow aspiring makeup professionals to gain experience at fashion shows, develop portfolios, strengthen practical skills, and gain exposure to professional working environments.

Her makeup artistry has also appeared in publications and magazine covers connected with New York and France.

As an educator and entrepreneur, Ángela has participated in events throughout the Latino community in the United States, using those opportunities to discuss makeup education, entrepreneurship, confidence, and professional development.

Bogotá International Book Fair Milestone

In 2026, Ángela participated in the Bogotá International Book Fair (FILBo), where she presented her work as an author and discussed her approach to connecting makeup education with women’s empowerment.

The appearance represented another step in Ángela’s effort to expand her work beyond traditional beauty services and develop a broader educational platform.

Her current work builds on that experience by integrating her published material with the REFLEJO™ Method, digital education, accessibility, and community engagement.

Bringing Beauty Education to Communities

Ángela is also strengthening partnerships and developing social initiatives aimed at providing free workshops focused on self-makeup, self-esteem, and empowerment.

The planned initiatives are intended to reach women in Afro-descendant, rural, and Indigenous communities in Colombia, as well as other populations that may have limited access to beauty education and related professional-development opportunities.

Through these programs, Ángela aims to apply the experience she has developed in the beauty industry to educational and community-based settings.

She has also begun collaborating with organizations and foundations that support women while developing a broader social-impact platform centered on education, leadership, inclusion, and dignity.

Connecting Beauty Education With Women’s Rights

Ángela recently participated in an event held within the context of the United Nations focused on education for peace and human rights.

She describes the experience as an important development in her work and one that strengthened her interest in participating in initiatives involving women’s rights, education, dignity, and access to opportunity.

Her long-term vision is to connect beauty education with wider social-impact initiatives and establish strategic partnerships capable of bringing those programs to additional communities.

For Ángela, women’s empowerment encompasses more than personal appearance. Her work increasingly addresses education, autonomy, inclusion, professional opportunity, dignity, and women’s ability to make informed decisions about their own lives.

An Immigrant Entrepreneur Building From New York

Ángela’s professional development also reflects her experience as a Colombian immigrant establishing a career in the United States.

Since moving to New York in 2020, she has worked to build her professional identity across makeup artistry, education, publishing, and entrepreneurship while developing Divina Makeup and the REFLEJO™ Method.

Her focus has gradually shifted from applying makeup for clients toward teaching women how to understand their individual features, develop practical skills, and approach their personal image with greater independence.

Through fashion, education, publishing, community initiatives, and international outreach, Ángela is continuing to develop a platform that brings together beauty education and social purpose.

About Ángela Rodríguez

Ángela Rodríguez is a Colombian-born author, professional makeup artist, Beauty Educator, entrepreneur, and creator of the REFLEJO™ Method. She is the founder of Divina Makeup and author of Maquíllate en 6 Pasos. Based in New York, her work focuses on self-makeup education, professional development, inclusion, accessibility, women’s empowerment, and community-focused initiatives.

Instagram: @divina.make.up

Media Contact

Ángela Rodríguez
Author | Beauty Educator | Creator of the REFLEJO™ Method
Founder, Divina Makeup
New York, United States
Instagram: @divina.make.up

Photo Credit: Photos accompanying this release were taken by New York-based photographer Dong Yang.

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BTI, Cornell Develop AI Tool to Map Hidden Universe of Small Molecules

Ithaca, NYResearchers at the Boyce Thompson Institute and Cornell University have developed AIMe (AI Molecule Explorer), a neuro-symbolic AI tool that predicts, organizes, and searches mass spectra for more than 100 million known small organic molecules—creating a searchable map of chemical space roughly a thousand times larger than existing experimental libraries. Applying AIMe to gut microbiome data, the team identified a previously unknown, ring-shaped polyamine compound also found in human fecal samples, and used the tool to annotate millions of unidentified spectra in a major public mass spectrometry database.

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Researchers at the Boyce Thompson Institute and Cornell University have developed AIMe (AI Molecule Explorer), a neuro-symbolic AI tool that predicts, organizes, and searches mass spectra for more than 100 million known small organic molecules—creating a searchable map of chemical space roughly a thousand times larger than existing experimental libraries. Applying AIMe to gut microbiome data, the team identified a previously unknown, ring-shaped polyamine compound also found in human fecal samples, and used the tool to annotate millions of unidentified spectra in a major public mass spectrometry database.

Ithaca, NY

Researchers at the Boyce Thompson Institute (BTI) and Cornell University unveiled AIMe (AI Molecule Explorer), a neuro-symbolic artificial intelligence tool that predicts and maps the mass spectra of more than 100 million known small organic molecules. The tool tackles a long-standing bottleneck in biomedical science—more than 80% of small molecules detected in a typical biological sample cannot be matched to a known structure—a gap that has stalled discoveries linking the gut microbiome, immunity, and metabolism.

 

Screenshot of AIMe results BTI, Cornell Develop AI Tool to Map Hidden Universe of Small Molecules

 

The work is a collaboration between Frank Schroeder, Professor at BTI and in Cornell’s Department of Chemistry and Chemical Biology, and Carla Gomes, Professor of Computing and Information Science and director of Cornell’s AI for Science Institute.

A different approach to an old problem

Mass spectrometry is the workhorse for small molecule identification used in a wide range of applications from toxicology to food analysis. When a compound is analyzed, the instrument fragments it and records the masses of the resulting pieces. That pattern of fragments, the tandem mass spectrum (or MS2 spectrum), functions as a molecular fingerprint. To identify an unknown compound, researchers compare its spectrum against a reference library of spectra from known compounds or develop hypotheses as to what the structure of a compound may be based on manual analysis of the fragmentation pattern.

The problem is that experimental reference libraries remain sparse, while expert, one-by-one interpretation is labor-intensive and slow. Collectively, available libraries cover fewer than 1% of known compounds, and resolving the structure of a single unknown can take days to months of iterative analysis and experimental validation. As a result, spectra without close library matches usually remain unannotated.

AIMe takes a different approach. Rather than waiting for experimental spectra to accumulate in libraries, it predicts spectra computationally—then organizes those predictions into a searchable resource called MS2KOSMOS. AIMe generated more than 800 million predicted spectra covering essentially all known small organic molecules in PubChem, the largest publicly available chemical database. That represents roughly a thousandfold expansion of searchable chemical space relative to existing experimental libraries.

“At the core of AIMe is DeepMS2Reasoner, a model that simulates how molecules fragment inside a mass spectrometer,” explained Gomes. “It builds fragmentation pathways step by step, using symbolic chemical rules to enumerate physically plausible fragmentation steps and a neural network to assign likelihoods to each step. The result is a predicted spectrum and an annotated map of how a molecule came apart—a feature that makes AIMe’s outputs interpretable in chemical terms, not just computationally useful.”

From mouse gut to human biology

To demonstrate what AIMe can do in practice, the researchers applied it to a comparative metabolomics dataset from mice. The experiment compared germ-free mice, animals raised without any gut microbiota, against mice with a normal complement of gut bacteria. Several thousand chemical features differed between the two groups, and most of the abundant ones could not be identified using standard methods.

The team used AIMe to query MS2KOSMOS with spectra from the 111 most abundant unidentified microbiota-dependent compounds. For roughly a third, AIMe retrieved close predicted spectral matches and related structural candidates, providing chemically interpretable leads for follow-up. For the rest, AIMe mapped the unknown spectra to molecular neighborhoods—sets of structurally related compounds whose shared fragmentation patterns could inform hypotheses about what the unknowns might be.

“Two compounds in particular became a case study in what AI-guided structure elucidation can accomplish,” said Schroeder. “Both produced spectra that suggested they were polyamine derivatives, a well-studied class of molecules, but the fragment patterns didn’t match anything previously described. Using AIMe’s output as a guide, our team assembled candidate structures combinatorially, predicted spectra for each candidate, and used the comparison to narrow the field.”

For the first compound, the best candidate was a linear putrescine derivative, which was then easily verified by synthesizing an authentic standard. For the second, the predicted spectra of potential candidates consistently failed to explain two prominent peaks—until the team expanded the search to include cyclized variants.

Synthesis confirmed what the predictions suggested. The second compound turned out to be a structurally unusual macrocyclic polyamine—a ring-shaped variant unlike any previously reported from mouse or human biology. Searches of a large public mass spectrometry database subsequently found the same compound in samples of human origin, detected in 57 of 99 human fecal samples examined.

Polyamines occupy an important position in biology. They sit at the intersection of diet, the gut microbiome, and immune function—and these findings suggest that the catalog of microbiota-dependent polyamines is far less complete than scientists assumed.

Annotation at scale

The researchers also tested AIMe at repository scale, applying it to more than 7 million spectral clusters from the Global Natural Products Social Molecular Networking database, one of the largest publicly available repositories of mass spectrometry data. Prior annotation efforts had annotated roughly 416,000 of those clusters. AIMe returned putative annotations for approximately 2.69 million, using the same similarity threshold applied in that earlier effort.

AIMe is accessible at https://www.cs.cornell.edu/gomes/udiscoverit/kosmos/ and the source code will be made publicly available upon publication of the study. The preprint is available on bioRxiv (DOI: 10.64898/2026.08.05.743095).

About the Boyce Thompson Institute (BTI)

As an independent nonprofit research institute affiliated with Cornell University, our scientists are committed to advancing solutions for global food security, agricultural sustainability, and human health. Through groundbreaking research, transformative education, and rapid translation of discoveries into real-world applications, BTI bridges fundamental plant and molecular science with practical impact. Discovery inspired by plants since 1924. Learn more at BTIscience.org.

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